Annapurna Pamreddy1, Nagender Reddy Panyala2,*
1Department of chemistry, Masaryk University, Brno, Czech Republic. 2Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Journal of Applied Bioanalysis. Vol.2. No.2. pages 52-75 (2016)
Published 15 April 2016. https://doi.org/10.17145/jab.16.009 | (ISSN 2405-710X)
- Sample preparation
- Separation science for intact proteins
- Liquid chromatography
- Reverse Phase Liquid Chromatography [RPLC]
- Intact proteins mass spectrometry
- Figures and Tables
- Fourier transform ion cyclotron resonance mass spectrometry
- Orbitrap mass spectrometry
- Fragmentation methods
- Collision-induced fragmentation
- Electron capture dissociation
- Electron transfer dissociation
- Differences between ECD and ETD
- Techniques and search engines used in top-down analysis
- Top-down proteomics applications
- TDP in snake venomic proteomics
- TDP in intact proteins analysis
- TDP in crosslink protein analysis
- TDP in Biomedical Research
- TDP in micro-organisms identification
- TDP in neurodegenerative diseases and cancer research
- TD in human body fluids analysis
- TDP in relative quantitation
- TDP in native mass spectrometry
- Challenges, limitations and perspectives
- Protein chromatography issues
- Lower sensitivity of TD analysis
- Limited number of bioinformatics tools
Redddy Panyala N . Lawrence Berkeley National Laboratory, 1 Cyclotron road, Berkeley, CA 94720. USA. Phone: +1-4404977898.
Pamreddy A and Panyala NR. Top-down proteomics: applications, recent developments and perspectives. J Appl Bioanal 2(2), 52-75 (2016).
Open-access and Copyright:
©2016 Pamreddy A and Panyala N. This article is an open access article distributed under the terms of the Creative Commons Attribution License (CC-BY) which permits any use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.
Funding/Manuscript writing assistance:
The authors have no financial support or funding to report and also declare that no writing assistance was utilized in the production of this article.
The authors have declared that no competing interest exist.
Received: 30 December 2015, Revised 22 March 2016, Accepted 4 April 2016
Now-a-days, top-down proteomics (TDP) is a booming approach for the analysis of intact proteins and it is attaining significant interest in the field of protein biology. The term has emerged as an alternative to the well-established, bottom-up strategies for analysis of peptide fragments derived from either enzymatically or chemically digestion of intact proteins. TDP is applied to mass spectrometric analysis of intact large biomolecules that are constituents of protein complexes and assemblies. This article delivers an overview of the methodologies in top-down mass spectrometry, mass spectrometry instrumentation and an extensive review of applications covering the venomics, biomedical research, protein biology including the analysis of protein post-translational modifications (PTMs), protein biophysics, and protein complexes. In addition, limitations of top-down proteomics, challenges and future directions of TDP are also discussed.
Top-down, protein biology, mass spectrometry, fragmentation techniques, data analysis.
In recent years the mass spectrometry (MS) ionization techniques such as ESI  and MALDI  have been applied for the detection of a wide variety of large biopolymers, such as proteins [3,4], lipids, and nucleic acids. Proteomics has significant number of applications in many fields, for instance, food science , clinical science, forensic science, biology and medical industry . There are two well-known proteomic approaches for various proteins analysis, i.e. bottom-up proteomics (BUP) and top-down proteomics (TDP). From earlier days, mass spectrometry-based proteomics has been carried out in a bottom-up fashion. In these BUP experiments, proteins are separated on the basis of their isoelectric point (pI) and molecular weight, respectively . Top-down mass spectrometry allows identification and characterization of proteins and protein networks by direct fragmentation. The ‘top-down’  approach provides far higher specificity at the expense of far higher experimental requirements by directly introducing the proteins into the mass spectrometer. The top-down method is being developed progressively in specific applications, with 18% of proteomics papers/posters at the 2007 meetings of American Society for Mass Spectrometry .
Top-down proteomics is different from the conventional bottom-up strategy of protein analysis which starts with intact mass measurement (Figure 1). In simple words, if anybody is interested just protein detection or its identification from a database, then bottom-up approach tends to be easier with a broad range of well-honed tools from the lion’s share of efforts from academic and as well as commercial vendors. However, if anyone is interested in the full characterization of protein including its amino acid sequence and modifications, then top-down strategy is the more efficient one. Bottom-up mass spectrometry has following disadvantages: a peptide or even several peptides may not be specific to an individual protein or protein form. Large regions of the protein may not be which can leave behind important information regarding PTMs, modifications and other sequence variations may occur on disperate peptides, causing their relation to one another to be lost following digestion. Top-down proteomics can eliminate these problems by the introduction of an intact protein into the mass spectrometer where both its intact and fragment ions masses are measured (Figure 1). This strategy usually covers 100% sequence coverage and full characterization of proteoforms including PTMs and sequence variations. Nowadays, a combination of both software and hardware is available to acquire the top-down data. Top-down proteomics in which a large number of intact proteins are fragmented directly in a mass spectrometer (without using a proteolytic enzyme)-is becoming more feasible every year. There are many more top-down studies have been reported in these years in comparison with the top-down studies prior to 2007. Some of them observed a few hundreds to even thousands of proteins in their top-down studies [10-14]. Figure 1 shows the workflow of both top-down and bottom-up proteomic approaches for the protein analysis using mass spectrometry. Figure 1 describes that traditional Bottom Up approach involves the digestion of proteins into peptides prior to introduction into the mass spectrometer where they are then detected and fragmented. In top-down mass spectrometry, the protein is ionized directly, allowing for improved sequence coverage and detection of post-translational modifications (PTM).
Currently many labs like Amgen and Amylin are using top-down strategy for the characterization of recombinant antibodies and endogenous secretory peptides. Many other labs are using top-down MS for the analysis of endogenous proteins like histones and biomarkers under 30 KDa and protein based therapeutics. In BUP experiments, proteins of interest are separated on the basis of their isoelectric point and molecular weight, respectively and followed by enzymatic digestion before MS analysis . This digestion can be performed either directly in solution or in-gel digestion after separation by 1D- or 2D gel electrophoresis. Top-down approach will provide protein sequence information directly without preliminary digestion. In contrast to bottom-up method, top-down method is attaining a pivotal position nowadays due to its versatile simplicity in the analysis of larger biomolecules. It has many advantages in comparison with bottom-up method, i.e., (i) no need of enzyme digestion (ii) high protein sequence coverage, etc. However, the current discovery mode TDMS has size limitation and it can’t go beyond a certain molecular weight (MW) and a typical top-down proteomics experiment in discovery mode, the MW cut-off is around ~30 kDa . However, this cut-off may go higher for targeted-mode TDP. In this top-down mass spectrometry method, intact proteins are fragmented directly (without using a proteolytic enzyme cleavage) in the mass spectrometer to attain both protein identification and characterization, even capturing information on combinatorial post-translational modifications. An emerging top-down MS-based proteomics approach provides an overview of all intact proteoforms, which has exclusive advantages for the identification and localization of PTMs and sequence variations [16-19]. The constitution of the new electron-based MS/MS techniques, like electron capture dissociation (ECD)  and electron transfer dissociation (ETD) , exemplify a substantial advancement for top-down by providing dependable methods for the localization and characterization of labile PTMs [20-27]. In the past 6-7 years, advanced instrumentation and software’s for the top-down analysis were developed, and top-down MS has also experienced a major improvement from refined separations of whole proteins in complex mixtures that have both high recovery and reproducibility. It might be possible to see a high throughput work flow which covers intact proteins and polypeptides up to 70 kDa in near future with the combination of advanced commercial MS instrumentation and data processing .
To perform top-down experiments using fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) instruments, it is necessary to have pure protein samples or simple mixtures. Even though one can use complex mixtures and separate the proteins by using a quadrupole mass analyzer that is hyphenated with the FTICR rather than HPLC. However, the dispersion of signals during ionization and the suppression of individual proteins reduce the signal-to-noise ratio. Thus, sample purification is usually an important step before analysis. Usually, during the electron-capture dissociation, formation of many fragments observed due to the cleavage at the backbone N–Cα bond in a highly but not completely nonspecific manner. Therefore, spectral averaging over a number of scans is usually needed to improve the signal-to-noise ratio.
Unlike the peptide analysis in a bottom-up approach, each protein is a unique case in top-down analysis. The fragmentation conditions are established in advance in bottom-up peptide identification and not changed during the LC-MS/MS analysis. But, in case of proteins, optimum results, however, are achieved by tuning the optimal conditions to fragment each parent protein ion. Thus, top-down is difficult to conduct with on-line HPLC separation. Due to this reason, TD has some difficulties for high throughput analysis wherein coupling of sample separation and FTICR with ECD is necessary but sometimes incompatible with the shorter time scales of LC separation and the longer times of FTICR-ECD spectral averaging. Hence, fraction collection (such as protein fractionation methods) is very often introduced between protein separation and FTICR measurement. Despite the difficulties, there is strong motivation to develop further top-down analysis by increasing the speed and mass resolving power of current instrument platforms. These improvements are required to enhance throughput to supplement bottom-up approaches that are inadequate for analyzing proteins with multiple modifications.
Separation science for intact proteins
Due to the high complexity of proteomic mixtures ranging from sub-organellar complexes to whole-cell proteomes, mass spectrometry is not solely sufficient to characterize a proteome. Therefore, efficient separation methods are necessary to reduce the sample complexity and increase the dynamic range of detection. Many separation methods can be applied offline or independent of the mass spectrometer . From the collection of eluted fractions followed by their injection into the mass spectrometer, more instrument time can be spent on collecting the data of a single protein or simple protein mixture. On the other hand, offline separations are more adaptable as they do not need to be mass spectrometry compatible. In comparison, online separations which are hyphenated with mass spectrometry, would allow increased throughput and reduced sample handling but with limitations to data acquisition and separation conditions. Taking into the consideration of the complexity of most proteome samples, multiple separations are required to achieve sufficient separation, often using an off-line approach coupled with an online separation.While there are many well-known separation methods available, based on the type of MS analysis, top-down or bottom-up, will determine what type of separation method is suitable for the better separation and as well as MS analysis. Usually separations are based on the protein-intrinsic parameters, which include charge, size and hydrophobicity, etc.
Liquid chromatography (LC) is one of the most common methods for the separation of intact proteins, peptides, and small molecules. The separation principle relies on differential partitioning of analytes between liquid mobile phase and a stationary phase. In many cases, LC can often hyphenated to electro spray ionization (ESI) and proved to be an efficient on-line analysis method . While there are variety of LC methods have been developed, reverse-phase LC (RPLC), hydrophobic interaction LC (HILIC) and ion exchange chromatography are three most common LC approaches applied for intact protein separations .
Reverse Phase Liquid Chromatography [RPLC]
RPLC uses a polar mobile phase and non-polar stationary phase which allows the most hydrophobic analytes elute first. Common stationary phases are alkyl chains (C4, C5, C8 and C18) linked to silica particles, where shorter alkyl chains are preferred for the intact protein separations as these shorter alkyl chains are less retentive and offer high recovery . Similarly, polymeric reverse phase materials (PLRP) offers increased mechanical strength, uniform hydrophobicity, and high recovery and PLRP materials have also been utilized widely for the intact protein separations [27,29,30]. In contrast to RPLC, hydrophobic interaction liquid chromatography (HILIC) uses a polar stationary phase and gradients increasing water content which results in the elution of more hydrophobic species first [31,32]. Modified histone forms separation using HILIC prior to top-down MS has been reported [33,34].
Ion exchange chromatography used differences in the charge of the analyte, while RPLC and HILIC rely primarily on differences in hydrophobicity to achieve separation. Ion exchange chromatography has been considered as a widespread separation method because its widespread familiarity and relatively high loading capacity. Increasing the mobile phase ionic strength is the key principle to elute the analyte from the charged stationary phase. Kellie et al. reported the use of a combination of ion exchange chromatography with reverse phase liquid chromatography and top-down mass spectrometry and they separated and identified 133 protein forms from human white blood cells . Similarly, a novel 3-dimension liquid chromatography strategy by coupling of hydrophobic interaction chromatography (HIC) and reverse phase chromatography with top-down MS separated and identified a total of 640 proteins from HEK 293 cell lysate protein fractions . On the other hand, chromatofocusing and solution isoelectric focusing (both utilizes pH gradient) are able to separate proteins with high isoelectric point correlation and are considered as alternative methods to salt gradient ion exchange chromatography for top-down proteomic separations [35,37].
Strong anion exchange coupled to RPLC-MS for the separation of intact proteins has also been reported for the study of E. Coli . Similarly, anion exchange RPLC has been used for the top-down study of yeast , human leukocytes , and Shewanella oneidensis . Chromatofocusing, a variant of ion-exchange chromatography which uses a pH change rather than ionic strength to perform elution, has been coupled with off-line RPLC for fractionation of proteins from Methanosarcina acetivorans . In contrast to conventional ion-exchange chromatography, chromatofocusing elutes proteins as a function of their isoelectric point [pI] for the intact proteins separation.
In addition to chromatography, electrophoresis is considered as an extremely popular approach for intact proteins separation which relies on the differential migration of proteins in an applied electric field [27,43]. The most common electrophoretic method is SDS PAGE, in which SDS coated proteins migrate through a polyacrylamide gel matrix in an electric field, achieving molecular weight based separation . This is commonly used in bottom-up proteomics via the digestion of proteins out of the gel and followed by on-line LC-MS run [45,46].This approach can be extended to two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) in which isoelectrofocusing is used as a 1st dimension separation and SDS-PAGE is as 2nd dimension separation of intact protein separation .
2D-PAGE is the most known platform for intact protein separation due to its unrivalled peak capacity; however, intact proteins extraction from gels results in low recovery. Therefore, separation of intact proteins prior to top-down MS analysis is necessary to fractionate the various proteins in solution phase. While conventional gel-based separation methods are not applicable to top-down proteomics, similar separation strategies such as tube gel electrophoresis have been developed. Continuous elution gel electrophoresis utilizes a tube gel column which can separate intact proteins which are then collected as they elute from the end of the gel column . Meng et al. demonstrated this approach for the fractionation of Saccharomyces cerevisiae proteome using acid-labile surfactant rather than using SDS, as it could be degraded upon acidification, limiting the downstream interferences. These fractions were further separated using offline RPLC on a C4 column before MS analysis. This tube gel electrophoresis further extended with the invention of gel-eluted liquid fraction entrapment electrophoresis (GELFREE). The GELFREE fractionation system is a novel protein fractionation system designed to maximize protein recovery during molecular weight based fractionation. The system consists of sample capacity cartridges with sample loading and sample collection chambers and a bench top GELFREE Fractionation Instrument. A constant voltage is applied between the anode and cathode reservoirs during the protein separation, and each protein mixture is electrophoretically driven from a loading chamber into a specially designed gel column gel. Proteins are concentrated into a tight band in a stacking gel, and separated based on their respective electrophoretic mobilities in a resolving gel. As proteins elute from the column, they are trapped and concentrated in liquid phase in the collection chamber [i.e., free of the gel]. This novel technology facilitates the quick and simple separation of several complex protein mixtures simultaneously. This technology offers broad mass range (5–100 kDa) of intact proteins separation on the basis of molecular weight, retaining important physiochemical properties of the analyte. This liquid phase entrapment of proteins provides for high recovery while eliminating the need for band or spot cutting, making the fractionation process highly reproducible. The GELFREE device first applied to a top-down study by Lee et al. 2009, in which SDS was used and then removed using methanol/chloroform/water precipitation prior to online nano-LCMS run [49,50]. Similar like GELFREE system, an approach MSWIFT  (membrane-separated wells for isoelectric focusing and trapping (Figure 2.) can also be employed for sample clean-up in bottom-up proteomics  and for removal of neutral buffering materials in protein sample . The major advantage of MSWIFT is that peptides/proteins with different isoelectricaI values are bracketed by membranes of fixed pH values, and the sample can be directly used for MS analysis unless the sample mixture is too complicated and needs further separation. This approach is well suitable for top-down analysis.
Usually, precursor ion having higher charge states is beneficial for better fragmentation. Evan Williams first reported that m-nitrobenzyl alcohol (mNBA) and glycerol can be included in the spray media to achieve “supercharging” of electro-sprayed protein ions . The proposed mechanism is that addition of the reagent into the sample solution enhances the surface tension of the droplets during evaporation of the solvent. Increased surface tension allows the droplets to accommodate more charges before reaching the Rayleigh limit . Loo’s group screened sulfolane(tetramethylene sulfone) and other reagents for supercharging of native proteins and noncovalent protein complexes .
Intact proteins mass spectrometry
A proteome wide-level intact protein detection and identification require a high performance mass spectrometer. Especially, high mass resolution and mass accuracy is essential to separate and accurately assign spectral peaks generated from complex protein precursor spectra containing multiple intact proteoforms. So extremely high resolution may be required to differentiate these undistinguishable peaks. Similarly, sensitivity plays also a key role as high molecular weight proteins will possess broad isotopic distributions, distributing the signal from a single protein across many peaks. In addition, a distribution of different charge states of analyte will be displayed in electro-spray ionization (ESI). From the combination of these two effects, the signal arising from an individual proteoform may be split into hundreds of channels, which reduces the signal at any mass-to-charge ratio (m/z). Perhaps, this becomes more prominent at high mass values as the number of isotopic peaks and charge states increase.
Usually, a protein must be first ionized well into the gas phase before its detection and fragmentation. So far, MALDI and ESI both are the two most common protein ionization techniques. MALDI generates single charged ion species and requires a mass analyzer capable of detecting high m/z species using time-of-flight (TOF) instrumentation. However, MALDI-TOF high throughput proteomics has limitations such as poor fragmentation, low resolution and the requirement of relatively purified samples and difficulty coupling to separations [57,58]. ESI usually generates multiple charged ion species and is considered as the preferred method for both peptides and intact proteins analysis. Taking advantage of mass accuracy and high mass resolution, top-down proteomic studies have majorly been implemented ESI coupled either with fourier transform ion cyclotron resonance (FTICR) or orbitrap mass analyzers and these two techniques will be the focus of further discussion.
Figures and Tables
[Click to enlarge]
Fourier transform ion cyclotron resonance mass spectrometry
Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) relies on the ion excitation at its cyclotron frequency within a strong magnetic field . A spatially coherent packet of ions were generated by this excitation, which orbit at an increased radius, allowing for the detection by monitoring the image current on a detection plate. The detected signal (also termed a transient) is converted from the time domain to the frequency domain through a Fourier transform and then to m/z through mass calibration.For the first time in 1989, ESI-FTICR-MS was used for the intact protein analysis with a detection of multiple charge states on a single protein . Further top-down studies demonstrated the isotopic resolution on proteins using a 2.8 Tesla instrument which showed accurate mass determination . The same instrument was also utilized to perform collision-induced dissociation (CID) and nozzle-skimmer dissociation (NSD)of ubiquitin, using the high resolving power of the instrument to determine charge state and identity of the fragment ions . An advanced hyphenation to FT-ICR technology, often focused on improving the analysis of intact proteins, included increases in magnetic field [63,64], an accumulation octopole for ion storage before transmission to the ICR cell [65,66], addition of a resolving quadrupole for mass selection . These modifications, allowing for increased sensitivity, dynamic range, and resolution were used on a 9.4 T instrument for the detection and identification of proteins from M. jannaschii and S. cerevisiae . This instrumentation design has been used for a variety of top-down proteomic studies [42, 69, 70].
A linear quadrupole ion trap/FTICR-mass spectrometer construction was first reported in 2004  and this instrument allowed for the storage and manipulation of ions from a continuous ion source in the linear trap before injecting them into the ICR cell. Mass accuracy was improved through the accurately controlling the number of ions (use of automatic gain control (AGC)) that are allowed to enter the ICR cell even from variable ion flux into the instrument which is typical of LC–MS. Fragmentation is also performed within the ion trap and fragment ions able to be detected using the high resolution and mass accuracy of the ICR analyzer or the ion trap speed. This instrument was commercialized using a 7 T (Tesla) magnet, achieving 100000 resolving power (m/z 400) and as well as <2 ppm mass accuracy without internal calibration. The use of 7 T LTQ-FTICR for top-down proteomics for the analysis of the S. cerevisiae proteome  and membrane proteins  has been reported. Similarly, a 12 T version of the instrument has been used for increased throughput studies using the automated on-line/off-line RPLC-MS platform for the study of human leukocytes , and M. acetivorans  as well as the GELFrEE platform for the analysis of S. cerevisiae . A 14.5 T version of the LTQ-FTICR instrument has also been reported, featuring approximately 4-fold higher mass accuracy and twice the resolving power of the 7 T instruments .
Orbitrap mass spectrometry
The Orbitrap mass analyzer, a new type of Fourier transform mass spectrometer was described in 2000 . This trap features a pair of axially symmetric electrodes: a central ‘‘spindle-like’’ electrode and an outer ‘‘barrel-like electrode’’. In this electric field, ions rotate around the central electrode while oscillating down the length of the electrode. The frequency of these oscillations is proportional to (m/z)-1/2. Image current on the outer electrodes is monitored and the resulting time domain signal is converted to frequency and then to m/z as in FTICR. Also similar to FTICR, the orbitrap mass analyzer has been coupled to a LTQ allowing for use of a continuous ion source (e.g. ESI), increasing mass accuracy with automatic gain control (AGC), and enabling efficient fragmentation . Coupling of the two analyzers was achieved by the use of a transfer octupole following the ion trap into a curved rf-only quadrupole (C-trap) used to eject ions axially towards the orbitrap analyzer. This new instrument was capable of obtaining 60000 resolving power (m/z 400) using a one second transient, achieving isotopic resolution of myoglobin and carbonic anhydrase.
In 2006, the use of the LTQ-orbitrap for more extensive analysis of intact proteins was first reported . The authors reported reproducible <10 ppm mass accuracy with this instrument on intact proteins and confidently identified the proteins using CID fragmentation (MS2 and MS3). The study of low molecular weight proteins from human blood including the quantitation of apolipoprotein proteoforms [79,80] using LTQ-orbitrap instrumentation. The LTQ-orbitrap was also used to distinguish several glycoforms from intact recombinant antibodies (150 kDa) and fragment the reduced light and heavy chains using CID . Similarly, the structural characterization of intact antibodies using higher-energy collisional dissociation (HCD) based high-resolution LTQ-orbitrap mass spectrometry has been reported . A new branded instrument LTQ Velos with significant modifications to the linear ion trap is also used for the top-down analysis . Improved ion injection optics allowed for 5-fold reduction in ion injection times and the use of two linear ion traps allowed for more efficient trapping and CID fragmentation in a higher pressure trap and higher resolution scanning in a lower pressure trap. The LTQ-orbitrap Velos has been used for the analysis of disease causing hemoglobin variants from dried blood droplets for potential clinical use . Antibodies have also been analyzed using this instrument, allowing for improved sequence coverage through the use of electron transfer dissociation (ETD) of the disulfide intact species . ETD is an electron-based fragmentation technique similar to ECD, but utilizes gaseous anions to transfer low-energy electrons to protonated analytes .
Michalski et al. reported a compact high-field orbitrap, coupled with an improved Velos PRO dual ion trap mass spectrometer and advanced signal processing, capable of a nearly 4-fold increase in resolution . Top-down proteomic analysis of H1299 human cancer cell line proteome using this instrument has also been reported and identified 690 unique proteins from the H1299 human cancer cell line . Similarly, top-down analysis and the identification of 1976 unique proteins from an H1299 cell line has also been reported . Other types of mass spectrometry instruments (e.g., time-of-flight mass spectrometers and ion-traps) can also be applied for intact proteins analysis, but till date they are less effective than FTICRs, and hybrid linear ion trap (LTQ)–orbitraps  or LTQ-FTICRs . In fact, the new-design orbitrap from Thermo Fisher utilizes a higher field orbitrap analyzer and improved ion-trap, providing another opportunity for top-down proteomics . The combination gives improved resolving power over older designs and higher speed, making it competitive with FTICR-based instruments . Fragmentation so far is by either ECD or ETD, but the relative effectiveness of ETD remains unknown for large proteins. Nevertheless, a significant advantage of orbitraps compared to FTICRs is that mass resolving power decreases as the square root of m/z not as its first power, making resolving power on orbitraps less sensitive to m/z . MALDI-TOF is less competitive than FTICR and orbitraps and several mass spectrometry groups utilized this approach for top-down analysis by employing the strategy of in-source decay (ISD) [88,92-94].
In proteomics study, gas phase chemistry has played a crucial role in mass spectrometry (MS). The ion dissociation or transformation to the characteristic tandem mass spectrometry spectra (MS2) fragmentation patterns is the key step generating the structure information of a protein or a peptide. Even though, collision-induced dissociation (CID) is the most widely applied fragmentation method for proteome identification and quantification analysis, it is not suitable for fragmentation of intact proteins, and peptides with labile post-translational modifications, such as phosphorylation and S-nitrosylation . Usually tandem mass spectrometry (MS/MS) involves the characterization of a precursor ion based on its fragments. MS/MS involves isolation of the parent ion followed by exposure to an external stimulus to induce controlled fragmentation. It is necessary to fragment the parent ion in a sequence-specific manner to gain sequence information about a peptide, i.e., to cleave between each amino acid residue with a single cleavage per intact peptide or protein ion. There are many different MS/MS fragmentation techniques. Most commonly used fragmentation techniques are (i) collision-induced dissociation (CID) [96,97] (ii) electron capture dissociation (ECD), and (iii) electron transfer dissociation (ETD). CID, ECD and ETD methods are used in top-down proteomic analysis.
Collision-induced dissociation (CID) is also referred as collision activated dissociation (CAD). It was first described by Jennings  and McLafferty and Bryce . In CID, parent ions are allowed to collide with neutral collision gas atoms or molecules (typically helium, nitrogen or argon which result the formation of ‘b’ and ‘y’ -type ions . Figure 3 shows the basic fragmentation behavior of CID (b- and y-ions), ECD and ETD (c and z ions). Usually, CID is more effective for small and low-charged peptides. The basic residues which are present in a peptide sequence may also prevent dissociation and generating few sequence ions. In addition, CID is not suitable for fragmentation of intact proteins, and peptides with labile post-translational modifications, such as phosphorylation and S-nitrosylation. In general, CID does not generate complete fragmentation in order to fully characterize proteins, but rather produces sufficient fragments or sequence tags to identify the protein. Furthermore, if the protein contains post-translational modifications (PTMs), low-energy CID most likely will not be appropriate to localize the modified site or the PTM. As the CID fragmentation method is found to be less effective fragmentation method for top-down analysis, there are two major fragmentation techniques that are used in top-down MS/MS analysis, i.e. electron capture dissociation (ECD) and electron transfer dissociation (ETD) fragmentation. However, top-down MS is still in its early developmental stage and in the process of overcoming several technical challenges. The inclusion of dissociation methods such as electron capture dissociation (ECD) greatly improves the top-down capabilities. ECD is especially utile for mapping labile post-translational modifications which are well-preserved during the ECD fragmentation process. Top-down MS with ECD has been successfully applied to cardiovascular research with unique benefits in separating the molecular complexity, quantifying modified protein forms, complete mapping of modifications with full sequence coverage, discovering unexpected modifications, and identifying and quantifying positional isomers and determining the order of multiple modifications [99-104]. The non-ergodic electron-based MS/MS techniques, ECD and electron transfer dissociation (ETD), are particularly suitable for the localization of labile PTMs like phosphorylation [100, 104]. Even though, there are several electron-based fragmentation methods available, only few fragmentation methods i.e. ECD and ETD fragmentation methods are discussed in this paper.
Electron capture dissociation
Electron-capture dissociation (ECD) is one of the fragmentation methods in which gas phase ions will be fragmented to elucidate the structure of the precursor compound. It was first time reported by Roman Zubarev and Neil Kelleher . The ECD technique involves the capture of electrons by positive precursor ions to form radical cations with subsequent specific cleavages for peptide N-Cα bonds (fragments). Figure 4 shows the ECD fragmentation scheme of protonated protein.[M + nH]n+ + e- → [ [M + nH](n-1)+]* → fragments
ECD is proved as a significant MS/MS technique for biomolecules analysis  predominantly for peptides and proteins. Major advantage of ECD for peptide/protein analysis is (i) ECD fragmentation results random cleavage. Therefore, sequence coverage tends to be higher for ECD than other fragmentation techniques [107,108], and ECD fragmentation efficiencies allow sequencing of longer peptides (20-30 residues), whereas CAD fragmentation is limited to 20 or fewer residues (ii) labile PTMs are retained on peptide/protein backbone fragments . In ECD, interested multiply charged ions are irradiated with low energy electrons (<0.2 eV) producing charge-reduced species, which dissociate along radical-driven pathways. The major product of electron capture by peptide [M+nH]n+ cations is typically the charge-reduced species [M+nH](n-1)+, that is, the precursor peptide ion that has captured an electron but has not dissociated. Often, that is accompanied by hydrogen loss, i.e. formation of [M+(n-1)H](n-1)+. The dominant peptide fragmentation pathways proceed via cleavage of the backbone N–Cα bond to give c-and fragment ions  (which may be accompanied by hydrogen atom transfer to give and, more commonly, z-fragment ions  and disulfide bonds . The fragments observed during ECD are shown in Figure 4. The mechanism by which c and z fragments are generated following electron capture has been, and remains, the subject of intense debate. The original ECD experiments utilized a heated metal filament, e.g., tungsten or barium. In order to produce sufficient fragments for detection, it was necessary to irradiate precursor ions for 30 s. As such, ECD was incompatible with LC and therefore unsuitable for bottom-up proteomics. The problem was addressed by the introduction of the heated dispenser cathode by Tsybin in 2001 . The timescale for ECD was reduced significantly (ms) and it became possible to couple ECD with online liquid chromatography [114-116].
Palmblad et al.  coupled LC with ECD for the analysis of a tryptic digest of bovine serum albumin and Davidson and Frego  demonstrated LC-ECD analysis of a pepsin digest of cytochrome c. Zubarev and co-workers demonstrated an approach on a modified LTQ FT hybrid linear ion trap FTICR in which a low resolution survey scan in the ion trap was followed by analysis of CID and ECD in the ICR cell . Creese and Cooper  undertook a direct comparison of LC-ECD-MS/MS with LC-CID-MS/MS revealed that, CID resulted in greater overall protein coverage, whereas ECD gave higher confidence in peptide sequence, thus showing the complementary nature of CID and ECD for bottom-up proteomics. ECD has been used frequently used for top-down analysis of proteins. The original paper by Zubarev et al.  showed that ECD of ubiquitin (8.6 kDa) resulted in cleavage of 50 of the 75 backbone N–Cα bonds; however, it was noted that ECD efficiency decreased with increasing protein size . From these above-mentioned achievements, ECD will be certainly considered as an extraordinary tool in the up-coming future. The electron-based dissociation techniques deliver valuable structural information on different types of precursor ions. Hence, based on the information, the structure of these ions can be deduced from the fragment ion distribution. Since the inception of ECD, many review articles have been published on ECD based ion electron reaction mechanism [108,118,119,106, 103].
Electron transfer dissociation
In a similar MS/MS fragmentation technique called electron-transfer dissociation the electrons are transferred by collision between the analyte cations and reagent anions [120-122]. ETD is known as electron transfer dissociation is one of the fragmentation methods in which fragmentation of the precursor ion will take place via the transfer of the electrons from an electron donor, reagent ion. Usually, in ETD method, reagent compounds such as fluoranthene, anthracene and azobenzene etc. were employed. ETD is a method of fragmenting ions in a mass spectrometer [100,101]. Similar to electron-capture dissociation; ETD induces fragmentation of cations (e.g. peptides or proteins) by transferring electrons to them. It was invented by Donald F. Hunt, Joshua Coon, John E. P. Syka and Jarrod Marto at the University of Virginia . ETD does not use free electrons but employs radical anions (e.g. anthracene or azobenzene) for this purpose:[M+nH]n+ + A– → [[M+nH](n-1)+]* +A → fragments
where A is the anion. ETD cleaves randomly along the peptide backbone (c-and z-ions) while side chains and modifications such as phosphorylation are left intact. The technique only works well for higher charge state ions (z>2), however relative to collision-induced dissociation (CID), ETD is advantageous for the fragmentation of longer peptides or even entire proteins. This makes the technique important for top-down proteomics .Much like ECD, ETD is believed to be particularly effective for peptides with modifications such as phosphorylation . Figure 5 shows the schematic view of ETD enabled Thermo LTQ Velos Pro mass spectrometer, ETD ion source, ETD reagent vials with heated inlets are located at the back side of the instrument.
Differences between ECD and ETD
Even though ECD has been proven to be a most useful and powerful fragmentation technique, ECD is not suitable to the all types of instruments. There is a restriction for ECD fragmentation i.e. low mass cut-off restrictions of the RF field in ECD, electrons cannot be captured in quadrupole ion traps. To overcome this restriction, specific anions (anthracene anions) were used as electron donors by Syka, Coon and Hunt to transfer electrons to multiple charged peptide cations, creating the electron transfer dissociation (ETD) technique . Preliminary data from a modified 3D ion trap showed that N–Cα or disulfide bonds were cleaved via ETD by interactions of multiply charged ions with anions (Figure 6). However, the ETD fragmentation technique was found to be lower efficient than that of ECD, because the recombination energy for ETD requires the electron to overcome the binding energy barrier from the anion before transferring to the cations. However, implementation of ETD in popular low-cost ion trap instrument was a significant discovery for the mass spectrometry society.
Techniques and search engines used in top-down analysis
Most popularly used search engines for identification of proteins via bottom-up approaches are MascotTM, SequestTM, X!tandemTM, PhenyxTM, and ProteinProspectorTM. In peptide mass fingerprinting experiments the protein identification is done by comparing experimental enzymatic digests m/z values with theoretical m/z values of silico protein digestion. Alternatively database searching with experimental MS/MS data sets of selected ions in the low mass range can also be used for identification. To decrease the number of complications these search engines are constantly improved . Although various proposals are under stage of experimentation, for instance to combine searches from various engines is still at early stage of experimentation. The software solutions for the analysis of intact protein fragmentation and top-down analysis are not fully developed. There is a huge demand for software that used for web-based identification and characterization of proteins by direct comparison of parent and fragment ions masses against elucidated proteomic databases. The first search engine that used for top-down identification of proteins was ProSight [127,128]. This software is a combination of search engines and a browser environment for the analysis of fragments above 10 kDa. ProSight focused on organism specific databases of protein and site-specific information. Fragment ion masses of high mass parent ions are used to perform searches against the constantly updated databases, which include post-translational modifications and single nucleotide polymorphisms (SNPs). Apart from ProSight, new web application tools have been developed. The most widely used web-based database search engine for bottom-up approach is Mascot due its probability-based scoring method and its fast operation algorithm, is limited to 16 kDa for precursor ion selection. BIG Mascot has been exclusively designed for top-down analysis and is therefore used for identification of large proteins fragmented via CID or ECD . Align spectra is another approach used to assign the different isomers of protein . This is an algorithm based approach that can find optimal alignments between an experimental mass issued from spectrum and a theoretical mass of protein sequence by using a constant number of mass values that correspond to post-translational modifications and mutations.
Top-down proteomics applications
From the review of published literature, it is well-known that top-down (TD) proteomics has various applications in different fields such as snake Venomic proteomics, intact protein analysis, cross-link protein analysis, cardiovascular, biomedical research, etc. Even though, TD has many applications in various biology fields, only few selected applications are given in this review.
TDP in snake venomic proteomics
The study on snake venoms has inspired many scientists to discover or develop number of pharmaceutical drugs, diagnostic kits, and research molecular tools. A nice review has been presented with details of different methodological approaches used so far to quantify all proteoforms present in any given snake venom [131,132]. The recent advancements in mass spectrometric instrumentation, dissociation strategies, and bioinformatic tools including top-down mass spectrometry instrumentation is increasingly attaining momentum in proteomic analysis [133-142]. More recently, Daniel P. et al was the ﬁrst person who applied top-down mass spectrometry for the snake (Indonesian King Cobra, Ophiophagus Hannah) Venomic proteomics applications .
TDP in intact proteins analysis
A rapid puriﬁcation, reliable quantiﬁcation, and comprehensive characterization of α-actin isoforms due to genetic variations together with PTMs was recently developed . It was reported that using top-down MALDI-FTICR-MS platform, the mass analysis of intact human serum peptides and small proteins with isotopic resolution up to ≈15 kDa and identiﬁed new proteoforms from an accurate measurement of mass distances . It was proved that mass spectrometry (MS)-based top-down proteomics, multi-dimensional liquid chromatography (MDLC) strategies can effectively separate intact proteins with high resolution and automation are highly desirable . Usually in proteomics, the major problem is the structural characterization of proteins expressed from the genome. To solve this problem, first we have to separate the interested protein from a complex mixture, identification of its DNA-predicted sequence, and the characterization of sequencing errors and posttranslational modifications. And finally, top-down mass spectrometry (MS) approach with electron capture dissociation (ECD) will be applied to characterize proteins. A similar approach for the characterization of proteins involved in the biosynthesis of thiamin, Coenzyme A, and the hydroxylation of proline residues in proteins has been reported .
TDP in crosslink protein analysis
Top-Down proteomics is getting more attention in the field of crosslink proteins analysis. Chemical cross linking hyphenated with mass spectrometry can be a powerful methodology for the identification of protein-protein interactions and for providing constraints on protein structures. However, enrichment of cross linked peptides is crucial to reduce sample complexity before mass spectrometric analysis. The heterogeneity of a complex protein mixture from biological samples becomes even more difficult to deal with when a person’s attention is shifted towards different protein complex topologies, transient interactions, or localization of protein-protein interactions (PPIs). A well-known method, i.e. chemical cross-linking of proteins, which gives not only identities of interactors, but could also provide information on the sites of interactions and interaction interfaces. Kruppa et al. reported the top-down mass spectrometric analysis of proteolytic digested crosslink proteins that have been covalently modified by bifunctional cross-linking reagents which can be useful for protein structure determination . Similarly, Novak et al. also has reported a top-down approach for the protein structure studies using FT mass spectrometry and chemical cross linking . Figure 7 shows the schematic illustration of cross-link proteins analysis using top-down approaches such as ECD and ETD, etc. for their structural identification using data analysis softwares such as proteome discoverer, Stavrox and Prosight softwares, etc. A nice review was published in 2006 which reported the use of top-down approaches for the three dimensional protein structure identification and as well as protein-protein interaction studies .
TDP in Biomedical Research
Top-down MS has been successfully applied to cardiovascular research with the unique advantages such as quantifying modified protein forms, complete mapping of protein modifications with full sequence coverage, discovering unexpected modifications, and identifying and quantifying positional isomers and determining the order of multiple modifications . Since top-down MS analyzes whole proteins instead of small peptides, it can easily reveal the full extent of molecular complexity of a protein . Top-down mass spectrometry was applied by Zhang et al. to study phosphorylation of cardiac troponin in a set of post-mortem and transplant human heart tissue samples with chronic heart failure . This group also characterized different phosphorylation sites and splice variants present in human and mouse cardiac tissues . An overview of the recent applications of top-down proteomics in biomedical research has been provided and outlined about the challenges and opportunities facing top-down proteomics strategies aimed at understanding and diagnosing human diseases . Using a top-down MS strategy, Ying Ge and co-workers linked the altered Post-translational modification of cardiac troponin-I (cTnI) to Heart Failure (HF)-associated contractile dysfunction in both animal models of HF and human clinical samples .
Recent times, the type II diabetes mellitus (T2D) cases have increased dramatically. Therefore, there is a significant interest in understanding the mechanisms contributing to the development of this condition . Borges et al. using a top-down proteomics approach identified a panel of PTM-based biomarkers to distinguish the spectrum of cardio vascular disease (CVD) and T2D co-morbidities .
TDP in micro-organisms identification
The recent top-down MS applications have focused on the role of bacterial protein PTMs in infection [156-158].Top-down MS was employed to study the PTM of intact pilin from the pathogenic bacterium Neisseria meningitidis . A study by Ansong et al. discovered a specific protein S-thiolation switch in Salmonella typhimurium in response to infection-like conditions . More recently, a top-down MS method for the rapid and high-confidence identification of intact Bacillus spore species was developed. In this method, fragment ion spectra of undigested [whole] protein biomarkers are obtained without the need for biomarker pre-fractionation, digestion, separation, and cleanup . Several proteins from E. coli, including an over expressed one directly from a cell lysate, using their charge stripping approach on an ESI/ion trap instrument were identified by McLuckey and co-workers . The ability of the top-down technique rapidly progressed to characterize eukaryotic proteins with more complicated combinations of PTMs, especially as improved hardware and software become widely available .
TDP in neurodegenerative diseases and cancer research
Neurodegenerative diseases treatment strategies focus only on symptom management . The top-down MS approach can be a preferred strategy for the elucidation of PTM-associated to disease mechanisms underlying neurodegenerative disorders [163-165]. A number of modified PTMs including phosphorylation and acetylation have been associated to the constitutive activation of cellular signaling pathways involved in the growth, proliferation, and survival of tumor cells. Perhaps, due to this link between the modified PTMs with tumor growth, several groups have already utilized top-down mass spectrometry for the identification of disease biomarkers and to study the effects of chemotherapeutics. [166-168].
TD in human body fluids analysis
Human body fluids are considered as great sources of biological markers, especially, as sources of potential protein biomarkers of the diseases. Analytical tools that permit rapid screening, low sample consumption, and accurate protein identification are of great significance in studies of complex biological samples and clinical diagnosis. Nowadays, mass spectrometry is considered as one of the most important analytical tools with applications in a wide variety of fields. Mass spectrometry, especially, top-down MS has been used to find post-translational modifications and to identify key functions of proteins in the human body. For example, a top-down LC/MS-based methodology for the separation and analysis of alterations in histone PTMs in primary leukemia cells from patients with refractory or chroniclymphocytic leukemia in response to treatment with depsipeptide, a histone deacetylase inhibitor was reported . Similarly, top-down proteomic analysis of Cerebrospinal fluid evidenced the potential biomarker role of LVV- and VV-hemorphin-7 in posterior cranial fossa pediatric brain tumors. Top-down MS identified two peptides, originally believed to be CSF contaminants from the blood, as LVV- and VV-hemorphin-7, two opioid peptides produced from the enzymatic cleavage of hemoglobin. .
Transthyretin (TTR) amyloidosis and hemoglobinopathies are the archetypes of molecular diseases where point mutation characterization is diagnostically critical. Théberge et al. have developed a top-down analytical methodology for variant and/or modified protein sequencing and examined the possibility of using this platform for the analysis of hemoglobin/TTR patient samples and evaluating the potential clinical applications. For this analysis, they used a commercial high resolution hybrid Orbitrap mass spectrometer (LTQ-Orbitrap™) with automated sample introduction. The presence of a variant is revealed by a mass shift consistent with the amino acid substitution in the protein sequence.Usually, Sickle cell disease and amyloidsis caused by single amino acid changes in hemoglobin and transthyretin (TTR). Therefore, it is essential the early detection of hemoglobin and TTR variants for the effective management of these diseases. A top-down MS platform utilizing affinity puriﬁcation and direct injection of diluted whole blood for the detection of TTR and hemoglobin variants was developed by Costello and coworkers .Also, Coelho Graca et al. developed a method for the rapid analysis of hemoglobin variants from patient blood samples .
Möhring T et al. described the top-down identification of endogenous peptides up to 9 kDa in cerebrospinal fluid and brain tissue by nanoelectrospray quadrupole time-of-flight tandem mass spectrometry. In this article, they described an approach using quadrupole time-of-flight mass spectrometry (TOF-MS) as a highly efficient mass spectrometric purification and identification tool after off-line decomplexation of biological samples by liquid chromatography . Post-translational modifications of proteins were identified by automated database searches and they identified thymosin beta-4 (5.0 kDa) and NPY (4.3 kDa) from rat hypothalamic tissue and ubiquitin (8.6 kDa) from human cerebrospinal fluid .
Tian et al. has developed a top-down MS method to identify different histone variants from a core histone extract. They identified 41 histone variants and they were also able to identify 20 different modiﬁcations sites on the different histones .Contrepois et al. used ultrahigh performance LC coupled to Orbitrap to quickly identify histone variants and PTMs in unfractionated core histones via top-down analysis .
TDP in relative quantitation
Quantitative information in proteomics is often required from the comparative studies between test (disease) and control (healthy) states. Usually, In the bottom-up proteomic approach, isobaric tag for relative and absolute quantitation (iTRAQ), isotope-coded affinity tags (ICAT), stable isotope labeling by amino acids of cell culture (SILAC), and related isotope-based labeling methods will be used to label peptides for MS measurements . Another strategy which is ‘‘label-free’’ strategy involves quantitation by counting the spectra taken for a given analyte (assuming that abundant analytes will be characterized by a larger number of spectra than low-level analytes) [175,176]. The information about protein isoforms is usually missing in bottom-up approach because it measures peptides. Top-down analysis provides quantitative data on different isoforms including individual and post-translation modifications. In addition, given that a protein modification gives several site-specific isoforms, a crude measure of the abundance of one isoform can be made by comparing the intensities of the peaks corresponding to unmodified and modified peptides . Zabrouskov et al.  characterized sequentially the relative step-wise deamidation of bovine ribonuclease A at five sites: Asn67,Asn71, Asn94, Asn 34, and Gln4. In more detail, Ying Ge’s group  considered the possible change of fragmentation efficiency owing to addition of a modification group to the protein and the variation of the modification sites. She introduced a quantitation scheme by using the fragments from the unmodified protein as ‘‘yardsticks’’ to normalize those unmodified fragments from the modified protein. Then the abundances of the modified fragments from the modified protein can be compared with those of unmodified fragments obtained in the same experiment.
TDP in native mass spectrometry
Native mass spectrometry (MS), or sometimes it is called as “native electro-spray ionization” allows proteins in their native or near-native states in solution to be introduced into the gas phase and investigated by mass spectrometry. This approach is found to be as a powerful tool to investigate protein complexes and allows the structural elucidation of protein complexes. It will not provide a structural model in atomic detail, but the sensitivity, speed, selectivity, dynamic mass range and mass accuracy of the analysis provides important advantages over other techniques. Its sensitivity permits the investigation of endogenous protein complexes, and another major benefit of the method is that it can simultaneously analyze several species in one spectrum. In simple words, if there is a heterogeneous population of protein complexes present in one sample, the interested one can be specifically isolated for further studies. Electro-spray ionization, a gentle ionization method allowing the preservation of quaternary protein structure, is the most popular technique to ionize the proteins/protein complexes of interest in this research field. Normally the protein complex is sprayed from a volatile buffer, compatible with the electro-spray process.A range of mass spectrometric approaches can be applied to investigate the biological systems. The exact mass of proteins can be determined, but also the stoichiometry of an assembly, its stability, dynamical behavior, conformation, subunit interaction sites and topological arrangement of the individual proteins within a complex. Zhang et al. reported a nice review  review which explained the background of native MS of protein complexes and described its strengths, taking photosynthetic pigment–protein complexes as examples.
Challenges, limitations and perspectives
Since 1998 to till date, many number of publications have published on “top-down approach” and this number is showing the capability of the approach. Nowadays, many more laboratories are adopting this approach. Its major strength is the utilization of electron-based fragmentation to determine various protein structures, structural modifications (for example, post-translational modifications and other changes (e.g., amino-acid substitutions) in proteins, protein-protein interactions, etc. However, this approach has also following limitations and challenges.
Protein chromatography issues
The major issue of protein chromatography is the solubility of proteins. Usually, working with peptides is rather easy due to their high solubility and are easily separated on any reversed phase column. In case of proteins, they are not the same. Large number of proteins is not easily soluble. Furthermore, LC-MS based protein chromatography is not friendlier in comparison with LC-MS based separation of peptides, in terms of peak shape, retention times and resolution. Because, larger proteins, on C4 reversed phase columns, are tend to be bind irreversibly to the phase with eluents used for the MS analysis. Due to these reasons, the most of the top-down (TD) applications deal with complex protein solutions that are preliminary separated by classical chromatographic methods. Samples are then collected and analyzed by TD after appropriate buffer exchange. The sample preparation workflow is complex and thus preventing TD from high throughput data production that remains Bottom-Up (BU) approach alive.
Lower sensitivity of TD analysis
The second limitation of top-down approach is the lower sensitivity for detection of PTMs than that of bottom-up approach. Till date, TD proteomics suffers from a sensitivity issue. This is due to the low ion counts for a single TD fragmentation event. Hence, the sample amount required for TD may be 10-100 fold more in comparison with BU experiments for the complex proteome analysis. Advanced technological is highly desired to address these issues. From this review, it is clear that protein separation methods coupled with top-down mass spectrometry will be a breakthrough to characterize therapeutic proteins. We hope that improvements in the technology and as well as methodologies might be on the way to resolve these issues with the new advanced instrumentation such as Orbitrap Elite, etc. The required technological developments were headed by the Kelleher group to realize the hope that top-down MS can be applied to solve problems in systems biology.
Limited number of bioinformatics tools
Till date, lack of sufficient bioinformatics tools for the Top-Down data analysis, management and interpretation in comparison with BU approach. The most convincing web-based softwares for TD data generated by ESI are ProSight PTM, ProSight PC and ProSight Lite softwares from Prof. Kelleher group. These tools allow the identification of proteins, both single and in mixtures, searching TD data against the most common online databases, with the possibility to detect PTMs, alternative splicing products and single nucleotide polymorphisms. In the near future, however, bioinformatics for ESI TD should gain increasing space. As an FTMS instrument working on a 20–30 kDa protein has the feasibility to accomplish an almost residue-by-residue de novo sequencing of the entire protein, to date, only a few solutions are available for the efficient interpretation of this huge amount of data. Due to the above-mentioned disadvantages, BU proteomics is still alive and will still produce important data flows for long time. It is clear from the recent discoveries that the unquestionable advantages of TD techniques are moving forward to reduce this gap and we hope that substantial improvements might be implemented in routine TD proteomics over the next few years.
The extension of ECD to other non-FTICR types of mass spectrometers should have advantages in expanding the mass spectrometry field. Recently, Voinov et al.  constructed a radiofrequency-free magnetic cell in which ECD products were generated and detected in a triple quadrupole instrument via the replacing the second quadrupole with this cell. This improvement brings ECD into the realm of beam-type instruments. By adjusting the voltages, ECD and CAD can be accomplished sequentially in the cell . The hyphenation of Q-TOF instruments with their shorter duty-cycle may provide a more convenient means to achieve high-throughput ECD top-down analysis. In–source atmospheric pressure (AP)-ECD is another potentially interesting advanced instrumentation . On other side, construction of high-field FTICR instruments for improved performance is already established with a 21 T magnet . In the meantime, the top-down technology will coexist with bottom-up and middle-down approaches for application to identification and biophysical investigation of proteins and other biomolecular entities.
From the above-mentioned top-down MS applications, it is clearly noted that TD mass spectrometry is well-suited for target-compound analysis. The protein biophysics research is growing in combination with hydrogen/deuterium exchange and other chemical labeling strategies to probe protein conformation and dynamics. Similarly, determination of the stoichiometry and compositions of macromolecular assemblies has significant importance in structural biology, because many biological functions are accomplished by proteins in complexes rather than by isolated proteins. From our scientific review of existing literature, it is concluded that ECD analysis of intact complexes using FTICR delivers both identification and structure information which holds significant importance in this direction. Also, a hyphenated ETD/ECD with the Q-TOF/ion mobility platform seems promising for the study of protein complexes; this integration gives cross sections, their changes for ETD/ECD fragments, and possibly CAD fragments to deduce structure. In addition, the high costs of TD setups play a vital role in the TD proteomics implementation in worldwide MS core facilities. However, TD has the caliber to elucidate protein structure down to such an accurate level that advanced discoveries in biomedical and biological sciences are to be expected in the next future.
1. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM.Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64–71(1989). [CrossRef]
2. Karas M, Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60, 2299–2301(1988). [CrossRef]
3. Henry KD, Williams ER, Wang BH, McLafferty FW, Shabanowitz J, Hunt DF. Fourier-transform mass spectrometry of large molecules by electrospray ionization. Proc Natl Acad Sci USA 86, 9075–9078 (1989).[CrossRef]
4. Tanaka K, Waki H, Ido Y, Akita S, Yoshida Y, Yoshida T. Protein and polymer analyses up to m /z 100,000 by laser ionization time-of-fl ight mass spectrometry. Rapid Commun Mass Spectrom 2, 151–153 (1988). [CrossRef]
5. Wang J,Li D, Dangott L J, Wu G.Proteomics and its role in nutrition research. J Nutr 136, 1759-1762 (2006).
6. Schulenborg T, Schmidt O, Van Hall A, Meyer, HE Hamacher M, Marcus K Proteomics in neurodegeneration – disease driven approaches. Neural Transm 113, 1055-1073 (2006). [CrossRef]
7. O’Farrel PH. High resolution two-dimensional electrophoresis of proteins. Biol Chem 250 (10), 4007-21 (1975).
8. Kelleher NL, Lin HY, Valaskovic GA, Aaserud DJ, Fridriksson EK, McLafferty FW. Top Down versus Bottom Up Protein Characterization by Tandem High-Resolution Mass Spectrometry. J Am Chem Soc 121 (4), 806–812 (1999). [CrossRef]
9. Kelleher NL. A growing number of labs are using many types of mass spectrometers to directly analyze intact proteins and to improve conversion of MS data into biological knowledge. Anal Chem 76 (11), 196A–203A (2004).
10. Bunger MK, Cargile BJ, Ngunjiri A, Bundy JL, Stephenson JL. Automated proteomics of E. coli via top-down electron-transfer dissociation mass spectrometry. Anal Chem 80(5), 1459–1467 (2008). [CrossRef]
11. Collier TS, Hawkridge AM, Georgianna DR, Payne GA, Muddiman DC. Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer. Anal Chem 80(13), 4994–5001 (2008).
12. Lee JE, Kellie JF, Tran JC, Tipton JD, Catherman AD, Thomas HM, Ahlf DR, Durbin KR, Vellaichamy A, Ntai I, Marshall AG, Kelleher NL.A robust two-dimensional separation for top-down tandem mass spectrometry of the low-mass proteome. J Am Soc Mass Spectrom 20(12), 2183–2191 (2009).
13. Tsai YS, Scherl A, Shaw JL, MacKay CL, Shaffer SA, Langridge-Smith PRR, Goodlett DR. Precursor ion independent algorithm for top-down shotgun proteomics. J Am Soc Mass Spectrom 20(11), 2154–2166 (2009).
14. Zhou F, Hanson TE, Johnston MV.Intact Protein Profiling of Chlorobium tepidum by Capillary Isoelectric Focusing, Reversed-Phase Liquid Chromatography, and Mass Spectrometry. Anal Chem 79 (18), 7145–7153 (2007).
15. Tran JC, Zamdborg L, Ahlf DR, Lee JE, Catherman AD, Durbin KR, Tipton JD, Vellaichamy A, Kellie JF, Li M, Wu C, Sweet SM, Early BP, Siuti N, LeDuc RD, Compton PD, Thomas PM, Kelleher NL. Nature 480, 254-8 (2011).
16. Siuti N., Kelleher N L, Decoding protein modiﬁcationsusing top-down mass spectrometry. Nat Methods 4, 817–821 (2007).
17. Zhang H, Ge Y,Comprehensive analysis of protein modiﬁcations by top-down mass spectrometry. Circ Cardiovasc Genet. 4(6), 711 (2011).
18. Tipton J D, Tran J C, Catherman A D, Ahlf D R, Durbin KR, and Kelleher NL .Analysis of intact protein isoforms by mass spectrometry. J Biol Chem 286(29), 25451–25458 (2011).
19. Armirotti A, Damonte G. Achievements and perspectives of top-down proteomics. Proteomics 10, 3566–76 (2010).
20. Zubarev RA, Haselmann KF, Budnik BA, Kjeldsen F, Jensen F. Towards an understanding of the mechanism of electron capture dissociation: a historical perspective and modern ideas. Eur J Mass Spectrom 8, 337-349 (2002).
21. Fornelli L, Parra J, Hartmer R, Stoermer C, Lubeck M, Tsybin YO. Top-down analysis of 30–80 kDa proteins by electron transfer dissociation time-of-flight mass spectrometry. Anal Bioanal Chem 405, 8505-8514 (2013).
22. Cooper HJ, Hakansson K, Marshall AG. The role of electron capture dissociation in biomolecular analysis. Mass Spectrom Rev 24, 201–22 (2005).
23. Ge Y, Lawhorn BG, ElNaggar M, Strauss E, Park JH, Begley TP, McLafferty FW. Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J Am Chem Soc 124(4), 672–678 (2002).
24. Ayaz-Guner S, Zhang J, Li L, Walker JW, Ge Y. In vivo phosphorylation site mapping in mouse cardiac troponin I by high resolution top-down electron capture dissociation mass spectrometry: Ser22/23 are the only sites basally phosphorylated. Biochemistry 48, 8161–70 (2009).
25. Ge Y, Rybakova IN, Xu Q, Moss RL. Top-down high-resolution mass spectrometry of cardiac myosin binding protein C revealed that truncation alters protein phosphorylation state. Proc Natl Acad Sci U SA 106, 12658–63 (2009).
26. Zhang J, Dong X, Hacker TA, Ge Y. Deciphering modifications in swine cardiac troponin I by top-down high-resolution tandem mass spectrometry. J Am Soc Mass Spectrom 21, 940–8 (2010).
27. Capriotti AL, Cavaliere C, Foglia P,SamperiR, LaganaA. Intact protein separation by chromatographic and/or electrophoretic techniques for top-down proteomics. J Chromatogr A 1218, 8760-8776 (2011).
28. Hiraoka, K. and Kudaka, I. (1990), Electrospray interface for liquid chromatography/mass spectrometry. Rapid Commun. Mass Spectrom 4: 519–526.
29. WengerCD, BoyneMT, FergusonJT, RobinsonDE, KelleherNL. Versatile Online− Offline Engine for Automated Acquisition of High-Resolution Tandem Mass Spectra. Anal Chem 80 (21), 8055-8063 (2008).
30. Vellaichamy A, TranJC,CathermanAD, LeeJE,Kellie JF, SweetSMM, ZamdborgL,ThomasPM, AhlfDR,DurbinKR,ValaskovicGA,KelleherNL. Size-Sorting Combined with Improved Nanocapillary-LC-MS for Identification of Intact Proteins up to 80 kDa. Anal Chem 82(4), 1234–1244 (2010).
31. Alpert AJ, Andrews PC.Cation-exchange chromatography of peptides on poly(2-sulfoethyl aspartamide)-silica. J Chromatograph 443, 85-96(1988).
32. AlpertAJ. Hydrophobic interaction chromatography of peptides as an alternative to reversed-phase chromatography. J Chromatography 444, 269-274(1988).
33. Garcia BA, Pesavento JJ, Mizzen CA, Kelleher NL.Pervasive combinatorial modification of histone H3 in human cells. Nat Methods 4, 487-489 (2007).
34. Pesavento JJ, GarciaBA, StreekyJA, Kelleher, Mizzen CA. Mild Performic Acid Oxidation EnhancesChromatographic and Top Down MassSpectrometric Analyses of Histones. Mol Cell Proteomics 6, 1510-1526 (2007).
35. Kellie JF, Tran JC, Lee JE, Ahlf DR, Thomas HM, Ntai I, Catherman AD, Durbin KR, ZamdborgL, Vellaichamy A,Thomas PM, Kelleher NL. The emerging process of Top Down mass spectrometry for protein analysis: biomarkers, protein-therapeutics, and achieving high throughput. Mol. BioSyst.6, 1532–1539 (2010).
36. Valeja SG, Xiu L, Gregorich ZR, Guner H, Jin S, Ge Y. Three dimensional liquid chromatography coupling ion exchange chromatography/hydrophobic interaction chromatography/reverse phase chromatography for effective protein separation in top-down proteomics. Anal Chem 87(10), 5363-5371 (2015).
37. Lubman DM, Kachman MT, Wang H, Gong S, Yan F, Hamler RL, O’Neil KA, Zhu K, Buchanan NS, Barder TJ.Two-dimensional liquid separations-mass mapping of proteins from human cancer cell lysates.J Chromatogr B Analyt Technol Biomed Life Sci. 782(1-2), 183-196 (2002).
38. Millea KM, Krull IS, Cohen SA, Gebler JC, Berger SJ. Integration of multidimensional chromatographic protein separations with a combined “top-down” and “bottom-up” proteomic strategy. J Proteome Res 5 (1), 135-146 (2006).
39. Parks BA, Jiang L, Thomas PM, Wenger CD, Roth MJ, Boyne MT, Burke PV, Kwast KE, Kelleher NL. Top-down proteomics on a chromatographic time scale using linear ion trap Fourier transform hybrid mass spectrometers. Anal Chem 79 (21), 7984-7991 (2007).
40. Roth MJ, Parks BA, Ferguson JT, Boyne MT II, Kelleher NL.“Proteotyping”: Population Proteomics of Human Leukocytes Using Top Down Mass Spectrometry. Anal Chem 80(8), 2857–2866 (2008).
.41. Sharma S, Simpson DC, Tolic N, Jaitly N, Mayampurath AM, Smith RD, Paša-Tolic L. Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry. J Proteome Res 6 (2), 602-610 (2007).
42. Patrie SM, Ferguson JT, Robinson DE, Whipple D, Rother M, Metcalf WW, Kelleher NL. Top down mass spectrometry of < 60-kDa proteins from Methanosarcina acetivorans using quadrupole FRMS with automated octopole collisionally activated dissociation. Mol Cell Proteomics 1, 14-25 (2006).
43. Rabilloud T. Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 1, 3-10 (2002).
44. Laemmli UK. Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4. Nature 227, 680-685 (1970).
45. Shevchenko A, Wilm M, Vorm O, MannM.Mass Spectrometric Sequencing of Proteins from Silver-Stained Polyacrylamide Gels. Anal Chem 68 (5), 850–858 (1996).
46. Wilm M, Shevchenko A, Hourhaeve T, Breit S, Schweigerer L, Fotsis T, Mann M. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379, 466-469 (1996).
47. Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R.Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci USA 97, 9390-9395 (2000).
48. Meng F, Cargile BJ, Patrie SM, Johnson JR, McLoughlin SM, Kelleher NL.Processing complex mixtures of intact proteins for direct analysis by mass spectrometry. Anal Chem 74(13), 2923-2929 (2002).
49. Lee JE, Kellie JF, Tran JC, Tipton JD, Catherman AD, Thomas HM, Ahlf DR, Durbin KR, Vellaichamy A, Ntai I, Marshall AG, Kelleher NL. A robust two-dimensional separation for top-down tandem mass spectrometry of the low-mass proteome. J Am Mass Spectrom 20 (12) 2183-2191 (2009).
50. Tran J C, Doucette AA. Multiplexed Size Separation of Intact Proteins in Solution Phase for Mass Spectrometry. Anal Chem 81, 6201-6209(2009).
51. Lim P, North R, VighG.Rapid isoelectric trapping in a micro preparative-scale multi-compartment electrolyzer. Electrophoresis. 28(12), 1851-9 (2007).
52. Cologna SM, Russell WK, Lim PJ, Vigh G, Russell DH. Combining isoelectric point-based fractionation, liquid chromatography and mass spectrometry to improve peptide detection and protein identification. J Am Soc Mass Spectrom 21(9), 1612-9 (2010).
53. Pai PJ, Cologna SM, Russell WK, Vigh G, Russell DH.Efficient electrophoretic method to remove neutral additives from protein solutions followed by mass spectrometry analysis. Anal Chem 83(7), 2814-8 (2011).
54. Iavarone AT, Jurchen JC, Williams ER.Supercharged protein and peptide ions formed by electrospray ionization. Anal Chem 73(7), 1455-60 (2001).
55. Iavarone AT, Williams ER.Mechanism of charging and supercharging molecules in electrospray ionization. J Am Chem Soc 125(8), 2319-27 (2003).
56. Lomeli SH, Peng IX, Yin S, Loo RR, Loo JA.New reagents for increasing ESI multiple charging of proteins and protein complexes. J Am Soc Mass Spectrom 21(1), 127-31 (2010).
57. Kelleher NL. Top-Down Proteomics. Anal Chem 76, 196A-203A (2004).
58. Abersold R, Mann M. Mass spectrometry-based proteomics. Nature 422, 198-207 (2003).
59. Marshall AG, Hendrickson CL, Jackson GS.Fourier Transform Ion Cyclotron Resonance mass spectrometry: a primer. Mass Spectrom Rev 17, 1-35 (1998).
60. Williams ER, Wang BH, McLafferty FW, Shabanowitz J, Hunt DF. . Fourier Transform mass spectrometry of large molecules by electro spray ionization. Proc Natl Acad Sci. USA 86,9075-9078 (1989).
61. Henry KD, McLafferty FW. Electrospray ionization with Fourier- transform mass spectrometry. Charge state assignment from resolved isotopic peaks. Org Mass Spectrom 25, 490-492 (1990).
62. Deguchi K, Ito H,Baba T,Hirabayashi A, Nakagawa H, Fumoto M, Hinou H, Nishimura SH. Structural analysis of O-glycopeptides employing negative- and positive-ion multi-stage mass spectra obtained by collision-induced and electron-capture dissociations in linear ion trap time-of-flight mass spectrometry. Rapid Commun Mass Spec 21(5) 691-698 (2007).
63. Cournoyer JJ, Pittman JL, Ivleva VB, Fallows E, Waskell L, Costello CE, O’Connor PB. Deamidation: Differentiation of aspartyl from isoaspartyl products in peptides by electron capture dissociation. Protein Sci 14, 452–463 (2005).
64. Williams JP, Creese AJ, Roper DR, Green BN and Cooper HJ. Hot Electron Capture DissociationDistinguishes Leucine from Isoleucine in aNovel Hemoglobin Variant, Hb Askew,54(D5)Val→Ile. J Am Soc Mass Spectrom 20, 1707–1713 (2009).
65. Yoo HJ, Wang N, Zhuang S, Song H, Håkansson K.Negative-Ion Electron Capture Dissociation: Radical-Driven Fragmentation of Charge-Increased Gaseous Peptide Anions J Am Chem Soc 133(42), 16790-16793 (2011).
66. Budnik BA, Haselmann KF, Zubarev RA.Electron Detachment Dissociation of Peptide Di-anions: An Electron-hole Recombination Phenomenon. Chem Phys Lett 342, 299–302 (2001).
67. Lioe H, O’Hair RAJ, Gronert S, Austin A, Reid GE. “Experimental and Theoretical proton affinities of Methionine, Methionine sulfoxide and their N- and C- terminal derivatives.”, Int J Mass Spectrom 267, 220–232 (2007).
68. Patrie SM, Charlebois JP, Whipple D, Kelleher NL, Hendrickson CL. Construction of a hybrid quadrupole/Fourier transform ion cyclotron resonance mass spectrometer for versatile MS/MS above 10 kDa. J Am Soc Mass Spectrom 15, 1099-1108 (2004).
69. Du Y, Meng F, Patrie SM, Miller LM, Kelleher NL. Improved Molecular Weight-Based Processing of Intact Proteins for Interrogation by Quadrupole-Enhanced FT MS/MS. J Proteome Res 3(4), 801-806 (2004).
70. Roth MJ, Forbes AJ, Boyne II MT, Kim YB, Robinson DB, Kelleher NL.Precise and Parallel Characterization of Coding Polymorphisms, Alternative Splicing, and Modifications in Human Proteins by Mass Spectrometry. Mol Cell Proteomics 4, 1002-1008 (2005).
71. Voinov VG, Deinzer ML, Barofsky DF. Radio-frequency-free cell for electron capture dissociation in tandem mass spectrometry. Anal Chem 81(3), 1238-43 (2009).
72. Ryan CM, Souda P, Bassilian S, Ujwal R, Zhang J, Abramson J, Ping P, Durazo A, Bowie JU, Hasan SS, Baniulis D, Cramer WA, Faull KF, Whitelegge JP. Post-translational modifications of integral membrane proteins resolved by top-down Fourier transform mass spectrometry with collisionally activated dissociation. Mol Cell Proteomics 9(5),791-803 (2010).
73. Ferguson JT, Wenger CD, Metcalf WW, and Kelleher NL. Top-Down Proteomics Reveals Novel Protein Forms Expressed in Methanosarcina acetivorans. J Am Soc Mass Spectrom 20(9), 1743-1750(2009).
74. Kellie JF, Catherman AD, Durbin KR, Tran JC, Tipton JD, Norris JL, Witkowski CE, Thomas PM, Kelleher NL. Robust analysis of the yeast proteome under 50 kDa by molecular-mass-based fractionation and top-down mass spectrometry. Anal Chem 84(1), 209-215 (2012).
75. Schaub TM, Hendrickson CL, Horning S, Quinn JP, Senko MW, Marshall AG.High-performance mass spectrometry: Fourier transform ion cyclotron resonance at 14.5 Tesla. Anal Chem 80(11), (2008) 3985-3990.
76. Makarov A. Electrostatic Axially Harmonic Orbital Trapping: A High-Performance Technique of Mass Analysis. Anal Chem 72(6), 1156-1162 (2000).
77. Makarov A, Denisov E, Kholomeev A, Balschun W , Lange O, Strupat K, Horning S. Performance Evaluation of a Hybrid Linear Ion Trap/Orbitrap Mass Spectrometer. Anal Chem 78(7), 2113-2120 (2006).
78. Macek B, Waanders LF, Olsen JV, Mann M. Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-Orbitrap mass spectrometer. Mol Cell Proteomics 5, 949–958 (2006).
79. Mazur MT, Cardasis HL, Spellman DS, Liaw A, Yates NA, Hendrickson RC. Quantitative analysis of intact apolipoproteins in human HDL by top-down differential mass spectrometry. Proc Natl Acad Sci USA 107(17), 7728-7733 (2010).
80. Cheon DH, Nam EJ, Park KH, Woo SJ, Lee HJ, Kim HC, Yang EG, Lee C, Lee JE. Comprehensive Analysis of Low-Molecular-Weight Human Plasma Proteome Using Top-Down Mass Spectrometry. J Proteome Res 15, 229–244 (2016).
81. Bondarenko PV, Second TP, Zabrouskov V, Makarov AA, Zhang Z. Mass Measurement and Top-Down HPLC/MS Analysis of Intact Monoclonal Antibodies on a Hybrid Linear Quadrupole Ion Trap–Orbitrap Mass Spectrometer. J Am Soc Mass Spectrom 20(8), 1415-1424 (2009).
82. Zhang J, Liu H, Katta V. Structural characterization of intact antibodies by high-resolution LTQ Orbitrap mass spectrometry. J Mass Spectrom 45(1), 112-120 (2010).
83. PekarSecond T, Blethrow JD, Schwartz JC, Merrihew GE, MacCoss MJ, Swaney DL, Russell JD, Coon JJ, Zabrouskov V. Dual-Pressure Linear Ion Trap Mass Spectrometer Improving the Analysis of Complex Protein Mixtures. Anal Chem 81(18), 7757-7765 (2009).
84. Edwards RL, Griffiths P, Bunch J, Cooper HJ.Top-Down Proteomics and Direct Surface Sampling of Neonatal Dried Blood Spots: Diagnosis of Unknown Hemoglobin Variants. J Am Mass Spectrom 23(11), 1921-1930 (2012).
85. Fornelli L, Damoc E, Thomas PM, Kelleher NL, Aizikov K, Denisov E, Makarov A, Tsybin YO. Analysis of Intact Monoclonal Antibody IgG1 by Electron Transfer Dissociation Orbitrap FTMS. Mol Cell Proteomics 11(12), 1758-1767 (2012).
86. Tsybin YO, Fornelli L, Stoermer C, Luebeck M, Parra J, Nallet S, Wurm FM, Hartmer R. Structural analysis of intact monoclonal antibodies by electron transfer dissociation mass spectrometry. Anal Chem 83(23), 8919-27 (2011).
87. Michalski A, Damoc E, Lange O, Denisov E, Nolting D, Müller M, Viner R, Schwartz J, Remes P, Belford M, Dunyach JJ, Cox J, Horning S, Mann M, Makarov A. Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes.Mol. Cell Proteomics 11(3), 1-11 (2012).
88. Reiber DC, Grover TA, Brown RS. Identifying Proteins Using Matrix-Assisted Laser Desorption/Ionization In-Source Fragmentation Data Combined with Database Searching. Anal Chem 70,673–683 (1998).
89. Catherman AD, Durbin KR, Ahlf DR, Early BP, Fellers RT, Tran JC, Thomas PM, Kelleher NL. Large-scale Top-down Proteomics of the Human Proteome: Membrane Proteins, Mitochondria, and Senescence. Mol Cell Proteomics 12(12), 3465-3473 (2013).
90. Solis SR.; GeY, Walker J W. Single amino acid sequence polymorphisms in rat cardiac troponin revealed by top-down tandem mass spectrometry. J Muscle Res Cell Motil 29, 203-212 (2008).
91. Compton P, Damoc E, Denisov E, Tran JE, Ahlf DE ,Wieghaus A, Senko MW, Horning SR, Makarov A, Kelleher NL. Proceedings of the 59th ASMS Conference on Mass Spectrometry and Allied Topics, 2011, Denver, Colorado.
92. Resemann A, Wunderlich D, Rothbauer U, WarscheidB,Leonhardt H, Kuhlmann JFK, Suckau D. Anal Chem 82, 3283–3292 (2010).
93. van Duijn E. Current Limitations in Native Mass Spectrometry Based Structural Biology. J Am Soc Mass Spectrom 21(6), 971–978 (2010).
94. Valaja SG, Tipton JD, Emmett MR, Marshall AG. New Reagents for Enhanced Liquid Chromatographic Separation and Charging of Intact Protein Ions for Electrospray Ionization Mass Spectrometry. Anal Chem 82 (17), 7515–7519 (2010).
95. Elviri L, ETD and ECD Mass Spectrometry Fragmentation for the Characterization of Protein Post Translational Modifications. In Tandem Mass Spectrometry-Applications and Principles, INTECH Open Access Publisher, 161-178 (2012).
96. Gauthier JW, Trautman TR, Jacobson DB.Sustained off-resonance irradiation for collision-activated dissociation involving Fourier transform mass spectrometry.Collision-activated dissociation technique that emulates infrared multiphoton dissociation.Anal Chim Acta 246, 211–225 (1991).
97. McLafferty FW, Bryce TA.Metastable-ion characteristics: characterization of isomeric molecules. Chem Commun 1215-1217 (1967).
98. Weiqun Li, Hendrickson CL, Emmett MR, Marshall AG. Identification of Intact Proteins in Mixtures by Alternated Capillary Liquid Chromatography Electrospray Ionization and LC ESI Infrared Multiphoton Dissociation Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal Chem, 71 (19), 4397–4402 (1999).
99. Zhang H, Ge Y. Comprehensive Analysis of Protein Modifications by Top-down Mass Spectrometry. Circ Cardiovasc Genet. 4, 711(2011).
100. Ayaz-Guner S, Zhang J, Li L, Walker JW, Ge Y, In vivo phosphorylation site mapping in mouse cardiac troponin I by high resolution top-down electron capture dissociation mass spectrometry: Ser22/23 are the only sites basally phosphorylated. Biochemistry 48, 8161–8170(2009).
101. Ge Y, Rybakova IN, Xu QG, Moss RL, Top-down high-resolution mass spectrometry of cardiac myosin binding protein c revealed that truncation alters protein phosphorylation state. Proc Natl Acad Sci USA 106, 12658–12663 (2009).
102. Zabrouskov V, Ge Y, Schwartz J, Walker JW. Unraveling molecular complexity of phosphorylated human cardiac troponin I by top down electron capture dissociation/electron transfer dissociation mass spectrometry. Mol Cell Proteomics 7, 1838–1849 (2008).
103. Zhang JA, Dong XT, Hacker TA, Ge Y. Deciphering modifications in swine cardiac troponin I by top-down high-resolution tandem mass spectrometry. J Am Soc Mass Spectrom. 21, 940– 948 (2010).
104. Xu F, Xu Q, Dong X, Guy M, Guner H, Hacker TA, Ge Y. Top-down high-resolution electron capture dissociation mass spectrometry for comprehensive characterization of post-translational modifications in rhesus monkey cardiac troponin I. Int J Mass Spectrom 305, 95-102 (2010).
105. Zubarev RA, Kelleher NL, McLafferty FW. Electron capture dissociation of multiply charged protein cations. A nonergodic process, J Am Chem Soc 120, 3265–3266(1998).
106. Cooper HJ, Håkansson K, Marshall AG. “The role of electron capture dissociation in biomolecular analysis”. Mass spectrom Rev 24 (2), 201–22(2005).
107. Axelsson J, Palmblad M, Håkansson K, Håkansson P.Electron capture dissociation of substance P using a commercially available Fourier transform ion cyclotron resonance mass spectrometer. Rapid Commun Mass Spectrom 13(6), 474-7 (1999).
108. Zubarev RA, Haselmann KF, Budnik BA, Kjeldsen F, Jensen F. Towards an understanding of the mechanism of electron capture dissociation: a historical perspective and modern ideas. Eur J Mass Spectrom 8, 337-349 (2002).
109. Kelleher NL, Zubarev RA, Bush K, Furie B, Furie BC, McLafferty FW, Walsh CT.Localization of labile posttranslational modifications by electron capture dissociation: the case of gamma-carboxyglutamicacid. Anal Chem 71(19), 4250-3 (1999).
110. Kalli A, Hess S. Electron capture dissociation of hydrogen-deficient peptide radical cations. J Am Soc Mass Spectrom. 23(10), 1729-40 (2012).
111. Savitski MM, Kjeldsen F, Nielsen ML, Zubarev RA.Hydrogen rearrangement to and from radical z fragments in electron capture dissociation of peptides. J Am Soc Mass Spectrom 18(1), 113-20 (2007).
112. Roepstorff P, Fohlman J. Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom 11(11), 601 (1984).
113. Tsybin YO, Hakansson P, Budnik BA, HaselmannKF,Kjeldsen F, Gorshkov F, Zubarev RA.Improved low-energy electron injection systems for high rate electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom 15, 1849–1854 (2001).
114. Davidson W, Frego L. Micro-high-performance liquid chromatography/Fourier transform mass spectrometry with electron-capture dissociation for the analysis of protein enzymatic digests. Rapid Commun Mass Spectrom. 16(10), 993–998 (2002).
115. Palmblad M, Tsybin YO, Ramstrom M, Bergquist J, Hakansson P. Liquid chromatography and electron-capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom 16, 988–992 (2002).
116. Cooper HJ, AkbarzadehS, Heath JK, Zeller M. Data-Dependent Electron Capture Dissociation FT−ICR Mass Spectrometry for Proteomic Analyses. J Proteome Res 4, 1538–1544 (2005).
117. Zubarev RA, Electron-capture dissociation tandem mass spectrometry. Curr Opin Biotech 15, 12–16 (2004).
118. Creese AJ, Cooper HJ. Liquid Chromatography Electron Capture Dissociation Tandem Mass Spectrometry (LC-ECD-MS/MS) versus Liquid Chromatography Collision-induced Dissociation Tandem Mass Spectrometry (LC-CID-MS/MS) for the Identification of Proteins. J Am Soc Mass Spectrom 18(5), 891–897 (2007).
119. Sleno L, Volmer DA. Ion activation methods for tandem mass spectrometry. J Mass Spectrom 39(10), 1091-1112 (2004).
120. Coon JJ, Ueberheide B, Syka JEP, Dryhurst DD, Ausio J, Shabanowitz J, Hunt DF. Protein identification using sequential ion/ion reactions and tandem mass spectrometry. P Natl Acad Sci USA 102(27), 9463-9468 (2005).
121. Zubarev RA, Zubarev AR, Savitski, MM. Electron capture/transfer versus collisionally activated/induced dissociations: Solo or duet? JASMS 19, 753–761 (2008).
122. HamidaneHB, Chiappe D, Hartmer R, Vorobyev A, Moniatte M, Tsybin YO. Electron capture and transfer dissociation: Peptide structure analysis at different ion internal energy levels. JASMS 20, 567-575 (2009).
123. US patent 7534622, Hunt DF, Coon JJ, Syka JEP, Marto JA. “Electron transfer dissociation for biopolymer sequence mass spectrometric analysis”, issued 2009-05-19.
124. McLuckey SA, Stephenson JL. “Ion/ion chemistry of high-mass multiply charged ions”. Mass Spectrom Rev 17 (6), 369–407(1998).
125. Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. “Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry”. Proc. Natl. Acad. Sci. U.S.A. 101 (26): 9528–33(2004).
126. Nesvizhskii AI. Protein identification by tandem mass spectrometry and sequence database searching. Methods Mol Biol 367, 87–119 (2007).
127. Taylor GK, Kim YB, Forbes AJ, Meng F, McCarthy R, KelleherNL. Web and database software for identification of intactproteins using “top down” mass spectrometry. Anal Chem 75, 4081–6 (2003).
128. Leduc RD, Kelleher NL. Using ProSight PTM and related tools for targeted protein identification and characterization with high mass accuracy tandem MS data. Curr Protoc Bioinformatics 19:13.6:13.6.1–13.6.28.(2007).
129. Karabacak NM, Li L, Tiwari A, Hayward LJ, Hong P, Easterling ML, Agar JN. Sensitive and specific identification of wild type and variant proteins from 8 to 669 kDa using top-downmassspectrometry. Mol Cell Proteomics, 8, 846–56 (2009).
130. Frank AM, Pesavento JJ, Mizzen CA, Kelleher NL, Pevzner PA.Interpreting top-down mass spectra using spectralalignment. Anal Chem 80(7), 2499–2505 (2008).
131. Petras D, Heiss P, Süssmuth RD, Calvete JJ. Venom Proteomics of Indonesian King Cobra, Ophiophagus hannah: Integrating Top-Down and Bottom-Up Approaches. J Proteome Res, 14 (6), 2539–2556 (2015).
132. Valente RH, AlvesNicolau C, Perales J, Costa Neves-Ferreira AGD. Snake Venom Proteopeptidomics: What Lies Behind the Curtain. Toxinology, DOI 10.1007/978-94-007-6649-56-1. (2014).
133. Kelleher NL, Thomas PM, Ntai I, Compton PD, LeDuc RD. Deep and quantitative top-down proteomics in clinical and translational research. Expert Rev Proteomics 11, 649−651 (2014).
134. Gault J, Malosse C, Machata S, Millien C, Podglajen I, Ploy MC, Costello CE, Dume nil G, Chamot-Rooke J. Complete post translational modification mapping of pathogenic Neisseria meningitidispilins requires top-down mass spectrometry. Proteomics 14, 1141−1151 (2014).
135. Catherman A, Skinner O, Kelleher N. Top down proteomics: facts and perspectives. Biochem Biophys Res Commun 445,683−693 (2014).
136. Dang X, Scotcher J, Wu S, Chu RK, Tolic N, Ntai I, Thomas PM, Fellers R T, Early BP, Zheng Y, Durbin KR, Leduc RD, Wolff JJ, Thompson CJ, Pan J, Han J, Shaw JB, Salisbury JP,EasterlingM, Borchers CH, Brodbelt JS, Agar JN, Pasa-Tolic L, Kelleher NL, YoungNL. The first pilot project of the consortium for top-down proteomics: a status report. Proteomics, 14, 1130−1140 (2014).
137. LeDuc RD, Fellers RT, Early BP, GreerJB, Thomas PM, Kelleher NL. The C-score: a Bayesian framework to sharply improve proteoform scoring in high-throughput top down proteomics. J Proteome Res 13, 3231−3240 (2014).
138. Durbin K, FellersR, Ntai I, Kelleher NL, Compton P. Autopilot: an online data acquisition control system for the enhanced high-throughput characterization of intact proteins. Anal Chem 86, 1485−1492 (2014).
139. Li Y, Compton P, JmNtaiTI,KelleherNL. Optimizing capillary electrophoresis for top-down proteomics of 30−80 kDa proteins. Proteomics 14, 1158−1164 (2014).
140. Cannon JR, Cammarata MB,Robotham SA, Cotham VC, Shaw JB, Fellers RT, Early BP,Thomas PM, Kelleher NL,Brodbelt JS. Ultravioletphoto dissociation for characterization of whole proteins on a chromatographic time scale. Anal Chem 86, 2185−2192(2014).
141. Corrêa-Netto C, Junqueira-de-Azevedo IL, Silva DA, Ho PL, Leitão-de-Araújo M, Alves,L.Sanz ML, Foguel D, ZingaliRB,Calvete IJ. Snake Venomics and venom gland transcriptomic analysis of Brazilian coral snakes, Micrurusaltirostris and M. corallinus. J Proteomics 74, 1795−1809(2011).
142. Fellers RT,Greer JB, Early BP, Yu X, LeDuc RD, Kelleher NL, Thomas PM. ProSight Lite: graphical software to analyze top-down mass spectrometry data. Proteomics 15(7), 1235-1238 (2014).
143. Daniel P, Paul H, Roderich D. Su, Juan JC. Venom Proteomics of Indonesian King Cobra, Ophiophagushannah: Integrating Top-Down and Bottom-Up Approaches. J Proteome Res 14, 2539−2556 (2015).
144. Chen YC, Ayaz-Guner S, Peng Y, Lane NM, Locher MR, Kohmoto T, Larsson L,Moss RL, Ge Y. E. Effective Top-Down LC/MS+ Method for Assessing Actin Isoforms as a Potential Cardiac Disease Marker. Anal Chem 87, 8399−8406 (2015).
145. Nicolardi S, Switzar L, Deelder AM, Palmblad M, Van der Burgt YEM. Top-Down MALDI-In-Source Decay-FTICR Mass Spectrometry of Isotopically Resolved Proteins. Anal Chem 87, 3429−3437 (2015).
146. Ge Y, Lawhorn BG, ElNaggar M, Strauss E, Park JH, Begley TP, McLafferty FW. Top Down Characterization of Larger Proteins (45 kDa) by Electron Capture Dissociation Mass Spectrometry. J Am Chem Soc 124, 672-678(2002).
147. Kruppa GH, Schoeniger J, Young MM. A top down approach to protein structural studies using chemical cross-linking and Fourier transform mass spectrometry. Rapid Commun Mass Spectrom 17, 155–162 (2003).
148. Novak P, Young MM, Schoeniger JS, Kruppa GH.A top-down approach to protein structure studies using chemical cross-linking and Fourier transform mass spectrometry. Eur J Mass Spectrom 9(6), 623-31 (2003).
149. Sinz A. Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein–protein interactions. Mass Spectrom Rev 25, 663–682(2006).
150. Zhang J, Guy MJ, Norman HS, Chen Y C, Xu Q, Dong X, Guner H, Wang S, Kohmoto T, Young KH, Moss RL, Ge Y.Top-Down Quantitative Proteomics Identified Phosphorylation of Cardiac Troponin I as a Candidate Biomarker for Chronic Heart Failure. J Proteome Res 10(9), 4054–4065 (2011).
151. Zhang J, Zhang H, Ayaz-Guner S, Chen Y C, Dong X, Xu Q, Ge Y. Phosphorylation, but not alternative splicing or proteolytic degradation, is conserved in human and mouse cardiac troponin T. Biochemistry 50, 6081–6092 (2011).
152. Gregorich ZR, Ge Y. Top-down proteomics in health and disease: Challenges and opportunities. Proteomics 14, 1195–1210 (2014).
153. Zhang J, Guy MJ, Norman HS, Chen YC, Xu Q, Dong X, Guner H, Wang S, Kohmoto T, Young KH, Moss RL, Ge Y. Top-down quantitative proteomics identiﬁed phosphorylation of cardiac troponin I as a candidate biomarker for chronic heart failure. J Proteome Res 10, 4054–4065 (2011).
154. Chen L, Magliano D J, Zimmet PZ. The worldwide epi- demiology of type 2 diabetes mellitus–present and future perspectives. Nat Rev Endocrinol 8, 228–236 (2012).
155. Borges CR, Oran PE,Buddi S, Jarvis JW, Schaab MR, Rehder DS, Rogers SP, Taylor T, Nelson RW. Building multidimensional biomarker views of type 2 diabetes on the basis of protein microheterogeneity. Clin Chem 57, 719–728 (2011).
156. AnsongC, Wu S, Meng D, Liu X, Brewer HM, Deatherage Kaiser BL, Nakayasu ES, Cort JR, Pevzner P, Smith RD, Heffron F, Adkins JN, Pasa-Tolic L. Top-down proteomics reveals a unique protein S-thiolationswitchin Salmonella typhimurium in response to infection-like conditions. Proc Natl Acad Sci USA 110(25),10153–10158 (2013).
157. Burnaevskiy N, Fox TG, Plymire DA, Ertelt JM, Weigele BA, Selyunin AS, Way SS, Patrie SM, Alto NM. Proteolytic elimination of N-myristoyl modiﬁcations by theShigella virulence factor Ipa. J Nat 496(7443), 106–109 (2013).
158. Chamot-Rooke J, Mikaty G, Malosse C, SoyerM,Dumont A, Gault J, Imhaus AF, Martin P, Trellet M, Clary G, Chafey P, Camoin L, Nilges M, Nassif X, Duménil G. Posttranslational modiﬁcation of pili upon cell contact triggers Nmeningitidisdissemination. Science 331(6018), 778–782 (2011).
159. Demirev PA, Feldman AB, Kowalski P,Lin JS.Top-Down Proteomics for Rapid Identification of Intact Microorganisms. Anal Chem. 77, 7455-7461 (2005).
160. Reid GE, Shang H, Hogan JM, Lee GU, McLuckeySA.Gas-phase concentration, purification, and identification of whole proteins from complex mixtures. J Am Chem Soc. 124, 7353–7362 (2002).
161. Pesavento JJ, Kim YB, Taylor GK, Kelleher NL. Shotgun Annotation of Histone Modifications: A New Approach for Streamlined Characterization of Proteins by Top Down Mass Spectrometry. J Am. Chem Soc 126, 3386–3387 (2004).
162. Reitz C, Brayne C, Mayeux R. Epidemiology of Alzheimer disease. Nat Rev Neurol 7, 137–152 (2011).
163. Auclair JR, Boggio KJ, Petsko GA, Ringe D, Agar JN. Strategies for stabilizing superoxide dismutase (SOD1),the protein destabilized in the most common form of famil-ial amyotrophic lateral sclerosis. Proc Natl Acad Sci USA 107, 21394–21399 (2010).
164. Molnar KS, Karabacak NM, Johnson JL, WangQ, Tiwari A, Hayward LJ, Coales SJ, Hamuro Y, Agar JN.A common property of amyotrophic lateral sclerosis-associated variants: destabilization of the copper/zinc superoxide dismutase electrostatic loop. J Biol Chem 284(45), 30965–30973 (2009).
165. Cabras T, Pisano E, Montaldo C, Giuca MR, Iavarone F, Zampino G, Castagnola M, MessanaI. Signiﬁcant modiﬁcations of the salivary proteome potentiallyassociatedwithcomplications of Downsyndromerevealed by top-down proteomics. Mol Cell Proteomics 12(7), 1844–1852 (2013).
166. Desiderio C, D’Angelo L, Rossetti D V, Iavarone F, Giardina B, Castagnola M, Massimi L, Tamburrini G, Di Rocco C.Cerebrospinal ﬂuid top-down proteomics evidenced the potential biomarker role of LVV- and VV-hemorphin-7 in posterior cranial fossa pediatric brain tumors. Proteomics12 (13), 2158–2166 (2012).
167. Zhang L, FreitasM, Wickham J, Parthun MR, Klisovic MI, Marcucci G, Byrd JC. Differential expression of histone post-translationalmodiﬁcations in acutemyeloid and chronic lymphocytic leukemia determined by high-pressure liquid chromatography and mass spectrometry. J Am Soc Mass Spectrom 15,77–86 (2004).
168. Arnaudo AM, BA Garcia. Proteomic characterization of novel histone post-translational modifications. Epigenetics & Chromatin 6, 24 (2013).
169. Theberge R, Infusini G, Tong W, McComb ME, Costello CE. Top-down analysis of small plasma proteinsusing an LTQ-Orbitrap. Potential for mass spectrometrybasedclinical assays for transthyretin and hemoglobin. Int J Mass Spectrom 300, 130–142 (2011).
170. Coelho Graça D, Lescuyer P, Clerici L, Tsybin YO, Hartmer R, Meyer M, Samii K, Hochstrasser DF, Scherl A. Electron transfer dissociation mass spectrometry of hemoglobin on clinical samples. J Am Soc Mass Spectrom 23(10), 1750–1756 (2012).
171. Möhring T, Kellmann M, Jürgens M, Schrader M. Top-down identification of endogenous peptides up to 9 kDa in cerebrospinal fluid and brain tissue by nanoelectrospray quadrupole time-of-flight tandem mass spectrometry. J Mass Spectrom 40, 214-26 (2005).
172. Tian Z, Zhao R, Tolic N, Moore RJ, Stenoien DL, RobinsonEW, SmithRD, Pasa-TolicL.Two-dimensional liquid chromatography system for online top-down mass spectrometry. Proteomics 10(20), 3610–3620 (2010).
173. Contrepois K, Ezan E, Mann C, Fenaille FJ. Ultra-High Performance Liquid Chromatography−Mass Spectrometry for the Fast Profiling of Histone Post-Translational Modifications. Proteome Res 9(10), 5501–5509 (2010).
174. Yates JR, Ruse CI, Nakorchevsky A.Proteomics by mass spectrometry: approaches, advances, and applications. Annual Review Biomed Eng 11(2009) 49-79.
175. PesaventoJJ , Mizzen CA, Kelleher NL. Quantitative Analysis of Modified Proteins and Their Positional Isomers by Tandem Mass Spectrometry: Human Histone H4. Anal Chem 78(13) 4271-4280 (2006).
176. Ntai I, Kim K, Fellers RT, Skinner OS, SmithIV AD, Early BP, Savaryn JP, LeDuc RD, Thomas PM, Kelleher NL. Applying Label-Free Quantitation to Top Down Proteomics. Anal Chem 86 (10), 4961–4968 (2014).
177. Zabrouskov V, Han X, Welker E, Zhai H, Lin C, Wijk KJV, ScheragaHA, McLafferty FW. Stepwise deamidation of ribonuclease A at five sites determined by top down mass spectrometry.B iochemistry 45(3), 987-992 (2006).
178. Zhang H, Cui W, Gross ML, Blankenship RE. Native mass spectrometry of photosynthetic pigment-protein complexes, FEBS Lett 587,1012-20 (2013).
179. Voinov VG, Deinzer ML, Barofsky DF. Radio-frequency-free cell for electron capture dissociation in tandem mass spectrometry. Anal Chem 81(3), 1238-43 (2009).
180. Voinov VG, Beckman JS, Deinzer ML, Barofsky DF. Electron-capture dissociation (ECD), collision-induced dissociation (CID) and ECD/CID in a linear radio-frequency-free magnetic cell. RapidCommun Mass Spectrom 23(18), 3028-30 (2009).
181. Robb DB, Rogalski JC, Kast J, Blades MW. Atmospheric pressure-electron capture dissociation of peptides using a modified PhotoSpray ion source. Rapid Commun Mass Spectrom 24(22), 3303-8 (2010).
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