A strategy for direct identification of protein S-nitrosylation sites by quadrupole time-of-flight mass spectrometry

S-nitrosylation of proteins serves an important role in regulating diverse cellular processes including signal transduction, DNA repair, and neurotransmission. Identification of S-nitrosylation sites is crucial for understanding the significance of this post-translational modification (PTM) in modulating the function of a protein. However, it is challenging to identify S-nitrosylation sites directly by mass spectrometric (MS) methods due to the labile nature of the S-NO bond. Here we describe a strategy for direct identification of protein S-nitrosylation sites in an electrospray ionization (ESI) quadrupole time-of-flight (QTOF) mass spectrometer without prior chemical derivatization of S-nitrosylated peptides. Both sample buffer composition and MS hardware parameters were carefully adjusted to ensure that S-nitrosylated peptide ions could be analyzed by the QTOF MS with optimal signal/noise ratios. It was crucial that the proteins were preserved in a sample solution containing 1 mM EDTA and 0.1 mM neocuproine at neutral pH. Proteins dissolved in this solution are amenable to in-solution tryptic digestion, which is important for the analysis of biological samples. S-nitrosylated peptides were effectively analyzed by LC/MS/MS on QTOF MS, with an optimized cone voltage of 20 V and collision energy of 4 V. We have successfully applied this method to thioredoxin, a key antioxidant protein, and identified within it an S-nitrosylation site at Cys73.     

Discovery of Post-Translational Modifications in Emiliania huxleyi

Emiliania huxleyi is a cosmopolitan coccolithophore that plays an essential role in global carbon and sulfur cycling, and contributes to marine cloud formation and climate regulation. Previously, the proteomic profile of Emiliania huxleyi was investigated using a three-dimensional separation strategy combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS). The current study reuses the MS/MS spectra obtained, for the global discovery of post-translational modifications (PTMs) in this species without specific enrichment methods. Twenty-five different PTM types were examined using Trans-Proteomic Pipeline (Comet and PeptideProphet). Overall, 13,483 PTMs were identified in 7421 proteins. Methylation was the most frequent PTM with more than 2800 modified sites, and lysine was the most frequently modified amino acid with more than 4000 PTMs. The number of proteins identified increased by 22.5% to 18,780 after performing the PTM search. Compared to intact peptides, the intensities of some modified peptides were superior or equivalent. The intensities of some proteins increased dramatically after the PTM search. Gene ontology analysis revealed that protein persulfidation was related to photosynthesis in Emiliania huxleyi. Additionally, various membrane proteins were found to be phosphorylated. Thus, our global PTM discovery platform provides an overview of PTMs in the species and prompts further studies to uncover their biological functions. The combination of a three-dimensional separation method with global PTM search is a promising approach for the identification and discovery of PTMs in other species.     

Dehydroalanine derived from cysteine is a common post-translational modification in human serum albumin

The conversion of a cysteine residue into dehydroalanine (DHA) in proteins was previously described. This post-translational modification (PTM) can be generated artificially as a result of heat and an alkaline environment. The presence of this PTM on human serum albumin (HSA) in plasma collected from healthy volunteers and critically ill patients as well as in commercially available HSA was studied. Using liquid chromatography/mass spectrometry (LC/MS) and matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS/MS) methods, a fragment containing DHA was identified in the trypsin digest of commercial HSA and isolated HSA from plasma. The sequence (RPC*FSALEVDETYVPK) corresponded to the expected molecular mass and fragmentation pattern of a tryptic peptide of HSA where the cysteine residue (cys487) was modified to DHA. The presence of this common PTM of HSA has potential effects on ligand binding to HSA, plasma clearance of this oxidized form of HSA, protein-protein interactions, and oxidation-reduction potential.     

Molecular mass determination of plasma-derived glycoproteins by ultraviolet matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with internal calibration

Human plasma-derived antithrombin III (AT-III), factor IX (FIX) and vitronectin (VN) were characterized as native glycoproteins and in their de-N-glycosylated form by means of MALDI mass spectrometry. The average molecular masses of the three complex glycoproteins were determined applying internal calibration with high-mass, well-defined protein calibrants. Internal calibration generated for the 47 kDa yeast protein enolase a mass precision in the continuous and delayed extraction mode of +/-0.12 and +/-0.022%, respectively. The achievable mass accuracy for such a high-mass, unmodified protein was in the range of 0.02% in the continuous mode, which turned out to be better than in the delayed extraction mode. Purification of all (glyco) proteins (even the calibration proteins) by means of ZipTip technology and direct elution with a solvent system containing the appropriate MALDI matrix turned out to be a prerequisite to measure the exact molecular masses with an internal calibration. The average molecular masses of the two different forms of AT-III, namely AT-III(alpha) and AT-III(beta), were shown to be 57.26 and 55.04 kDa, respectively. The 2.22 kDa mass difference is attributed to the known difference in carbohydrate content at one specific site (Asn-135). After exhaustive de-N-glycosylation (by means of PNGase F) of the alpha- and beta-form and subsequent MALDI-MS analysis, average molecular masses of 48.96 and 48.97 kDa, respectively, were obtained. These values are in good agreement (-0.15%) with the calculated molecular mass (49.039 kDa) of the protein part based on SwissProt data. The molecular mass of the heavily post-translational modified glycoprotein FIX was found to be 53.75 kDa with a peak width at 10% peak height of 4.5 kDa, because of the presence of many different posttranslational modifications (N- and O-glycosylation at multiple sites, sulfation, phosphorylation, hydroxylation and numerous gamma-carboxyglutamic acids). MALDI-MS molecular mass determination of the native, size-exclusion chromatography-purified, VN sample revealed that the glycoprotein was present as dimer with molecular mass of 117.74 kDa, which could be corroborated by non-reducing SDS-PAGE. After sample treatment with guanidine hydrochloride and mass spectrometric analysis, a single, new main component was detected. The molecular mass turned out to be 59.45 kDa, representing the monomeric form of VN, known as V75. The determined molecular mass value was shown to be on one hand lower than from SDS-PAGE and on the other higher than the calculated amino acid sequence molecular mass (52 277 Da), pointing to the well-known SDS-PAGE bias and to considerable post-translational modifications. Further treatment of the sample with a reducing agent and subsequent MALDI-MS revealed two new components with molecular masses of 49.85 and 9.41 kDa, corresponding to V65 and V10 subunits of VN. PNGase F digest of the V75 and V65 units and MS analysis, exhibiting a molecular mass reduction of 6.37 kDa in both cases, verified the presence of a considerable amount of N-glycans.     

New and automated MS<Superscript>n</Superscript> approaches for top-down identification of modified proteins

An automated top-down approach including data-dependent MS(3) experiment for protein identification/characterization is described. A mixture of wild-type yeast proteins has been separated on-line using reverse-phase liquid chromatography and introduced into a hybrid linear ion trap (LTQ) Fourier transform ion cylclotron resonance (FTICR) mass spectrometer, where the most abundant molecular ions were automatically isolated and fragmented. The MS(2) spectra were interpreted by an automated algorithm and the resulting fragment mass values were uploaded to the ProSight PTM search engine to identify three yeast proteins, two of which were found to be modified. Subsequent MS(3) analyses pinpointed the location of these modifications. In addition, data-dependent MS(3) experiments were performed on standard proteins and wild-type yeast proteins using the stand alone linear trap mass spectrometer. Initially, the most abundant molecular ions underwent collisionally activated dissociation, followed by data-dependent dissociation of only those MS(2) fragment ions for which a charge state could be automatically determined. The resulting spectra were processed to identify amino acid sequence tags in a robust fashion. New hybrid search modes utilized the MS(3) sequence tag and the absolute mass values of the MS(2) fragment ions to collectively provide unambiguous identification of the standard and wild-type yeast proteins from custom databases harboring a large number of post-translational modifications populated in a combinatorial fashion.     

色谱保留时间在蛋白质组研究中的应用

液相色谱与串联质谱联用(LC-MS/MS)技术是蛋白质组学研究中的常见方法。保留时间作为独立于质谱信息的参数已经被用于蛋白质的鉴定和定量工作中。在多肽鉴定领域,多肽的色谱保留时间预测与常规的二级串联质谱数据库搜索算法结合可以提高鉴定的可信度。鉴定的灵敏度也可以通过匹配多次LC-MS实验中具有相同精确质量数和保留时间的峰而提高。另一方面,由于色谱条件的微小改变即会引起保留时间的变化,因此对多次实验结果进行保留时间比对是进行非标记定量的不可或缺的步骤。另外,联合保留时间偏移和质量数信息还可以进行蛋白质翻译后修饰(post-translational modification, PTM)的鉴定。     

On-Line HPLC-UV-mass spectrometry and tandem mass spectrometry for the rapid delineation and characterization of differences in complex mixtures: a case study using toxic oil variants

An integrated differential approach to the characterization of complex mixtures is presented which includes the targeting of liquid chromatography (LC) peaks for identification using characteristic UV adsorption of the LC peak, subsequent molecular weight and formula determination using accurate mass LC mass spectrometry (MS), and structure characterization using accurate mass LC-tandem mass spectrometry. The use of differential UV adsorption aids in narrowing the scope of the study to only specific peaks of interest. Accurate mass measurement of the molecular ion species provides molecular weight information as well as atomic composition information. The tandem MS (MS/MS) spectra provide fragmentation information which allows for structural characterization of each component. Accurate mass assignment of each of the fragment ions in the MS/MS spectrum provides atomic composition for each of the fragment ions and thus further aids in the structural characterization. These experiments are facilitated through the use of on-line LC-MS and LC-MS/MS with in-line UV detection. A synthetic toxic oil (STO) related to Toxic Oil Syndrome is studied with a focus on possible contaminants resulting from the interaction of aniline, used as a denaturant, with the normal components of the oil. A differential analysis between the STO and a control oil is performed. LC peaks were targeted using UV absorbance to indicate the possible presence of the aniline moiety. Further differential analysis was performed through the determination of the MS signals associated with each component separated on the LC. Finally, the MS/MS data was also used to determine if the fragmentation of the targeted components indicated the presence of aniline. The MS/MS and accurate mass data were used to assign the structures for the targeted components.     

Multitechnique mass-spectrometric approach for the detection of bovine glutathione peroxidase selenoprotein: focus on the selenopeptide

Glutathione peroxidase (isolated from bovine erythrocytes) and its behaviour during alkylation and enzymatic digestion were studied by various hyphenated techniques: gel electrophoresis–laser ablation (LA) inductively coupled plasma (ICP) mass spectrometry (MS), size-exclusion liquid chromatography–ICP MS, capillary high-performance liquid chromatography (capHPLC)–ICP MS, matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) MS, electrospray MS, and nanoHPLC–electrospray ionization (ESI) MS/MS. ESI TOF MS and MALDI TOF MS allowed the determination of the molecular mass but could not confirm the presence of selenium in the protein. The purity of the protein with respect to selenium species could be evaluated by LA ICP MS and size-exclusion chromatography (SEC)–ICP MS under denaturating and nondenaturating conditions, respectively. SEC–ICP MS and capHPLC–ICP MS turned out to be valuable techniques to study the enzymolysis efficiency, miscleavage and artefact formation during derivatization and tryptic digestion. For the first time the parallel ICP MS and ESI MS/MS data are reported for the selenocysteine-containing peptide extracted from the gel; capHPLC–ICP MS allowed the sensitive detection of the selenopeptide regardless of the matrix and nanoHPLC–electrospray made possible its identification. Figure Eye catching image Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Development of isotope dilution-liquid chromatography/mass spectrometry combined with standard addition techniques for the accurate determination of tocopherols in infant formula

During the development of isotope dilution-liquid chromatography/mass spectrometry (ID-LC/MS) for tocopherol analysis in infant formula, biased measurement results were observed when deuterium-labeled tocopherols were used as internal standards. It turned out that the biases came from intermolecular H/D exchange and intramolecular H/D scrambling of internal standards in sample preparation processes. Degrees of H/D exchange and scrambling showed considerable dependence on sample matrix. Standard addition-isotope dilution mass spectrometry (SA-IDMS) based on LC/MS was developed in this study to overcome the shortcomings of using deuterium-labeled internal standards while the inherent advantage of isotope dilution techniques is utilized for the accurate recovery correction in sample preparation processes. Details of experimental scheme, calculation equation, and uncertainty evaluation scheme are described in this article. The proposed SA-IDMS method was applied to several infant formula samples to test its validity. The method was proven to have a higher-order metrological quality with providing very accurate and precise measurement results.     

Matrix-assisted ionization vacuum for protein detection,fragmentation and PTM analysis on a high resolution linear ion trap-orbitrap platform

Matrix-assisted ionization vacuum (MAIV) is a novel ionization technique that generates multiply charged ions in vacuum without the use of laser ablation or high voltage. MAIV can be achieved in intermediate-vacuum and high-vacuum matrix-assisted laser desorption/ionization (MALDI) sources and electrospray ionization (ESI) sources without instrument modification. Herein, we adapt MAIV onto the MALDI-LTQ-Orbitrap XL platform for biomolecule analysis. As an attractive alternative to MALDI for in solution and in situ analysis of biomolecules, MAIV coupling to high resolution and accurate mass (HRAM) MS instrument has successfully expanded the mass detection range and improved the fragmentation efficiency due to the generation of multiply charged ions. Additionally, the softness of MAIV enables potential application in labile post-translational modification (PTM) analysis. In this study, proteins as large as 18.7 kDa were detected with up to 18 charges; intact peptides with labile PTM were well preserved during the ionization process and characterized MS/MS; peptides and proteins in complex tissue samples were detected and identified both in liquid extracts and in situ. Moreover, we demonstrated that this method facilitates MS/MS analysis with improved fragmentation efficiency compared to MALDI-MS/MS.     

Two-dimensional supercritical fluid chromatography/mass spectrometry for the enantiomeric analysis and purification of pharmaceutical samples

A new analytical two-dimensional supercritical fluid chromatography/mass spectrometry system (2D SFC/SFC/MS) has been designed and implemented to enhance the efficiency and quality of analytical support in drug discovery. The system consists of a Berger analytical SFC pump and a modifier pump, a Waters ZQ 2000 mass spectrometer, a set of switching valves, and a custom software program. The system integrates achiral and chiral separations into a single run to perform enantiomeric analysis and separation of a racemic compound from a complex mixture without prior clean up. The achiral chromatography in the first dimension separates the racemate from all other impurities, such as un-reacted starting materials and by-products. Mass-triggered fractionation is used to selectively fractionate the targeted racemic compound based on its molecular weight. The purified racemate from the achiral chromatography in the first dimension is then transferred to the chiral column in the second dimension to conduct the enantiomeric separation and analysis. A control software program, we coined SFC2D, was developed and integrated with MassLynx to retrieve acquisition status, current sample information, and real time mass spectrometric data as they are acquired. The SFC2D program also monitors the target ion signal to carry out mass-triggered fractionation by switching the valve to fractionate the desired peak. The 2D SFC/SFC/MS system uses one CO(2) pump and one modifier pump for both first and second dimension chromatographic separations using either gradient or isocratic elution. Similarly, a preparative 2D SFC/SFC/MS system has been constructed by modifying an existing Waters preparative LC/MS system. All components except the back pressure regulator are from the original LC/MS system. Applications of the 2D SFC/SFC/MS methods to the separation and the analysis of racemic pharmaceutical samples in complex mixtures demonstrated that an achiral separation (in first dimension) and a chiral separation (in second dimension) can be successfully combined into a single, streamlined process both in analytical and preparative scale.     

尺寸排阻-反相液相色谱-质谱联用技术在大鼠肾脏翻译后修饰蛋白质鉴定中的应用

LC-MS联用技术在蛋白质组学研究中具有重要的作用,但是在复杂的生物体系中,由于样品的高度复杂性和其中蛋白质含量的巨大差异,执行全面且无倾向的蛋白质组分析是一项挑战。因此,在液相色谱分离中采用基于不同原理的色谱分离方法来降低蛋白质样本的复杂度,并对微量蛋白质进行富集,对后续采用质谱方法进行信息的采集和深入分析至关重要。在这里我们开发了一种基于尺寸排阻色谱(SEC)与反相液相色谱(RPLC)结合的新方法来进行复杂体系蛋白质的分离和鉴定,特别是对于微量蛋白质的分析。首先使用SEC对蛋白质进行分离和富集,并酶解成多肽,再通过RPLC-MS联用的方法对酶解后的多肽进行分离和鉴定。结果显示使用上述方法可以有效降低蛋白质样本的复杂度,并有效提高微量蛋白质的鉴定能力,可从大鼠肾脏鉴定出23621个肽段及1345个蛋白质,比常规的二维强阳离子交换-反相液相色谱法(2D SCX-RPLC)鉴定到的肽段及蛋白质分别多出69%及27%。此外,该方法对肾脏翻译后修饰(PTM)蛋白质的鉴定显示出更多的优势,翻译后修饰的多肽鉴定率显著增加,特别是磷酸化肽段的鉴定效率可达到靶向富集策略的水平。在此展示的SEC-RPLC-MS可以更好地了解蛋白质翻译后修饰对肾脏的影响,最终将有助于增加我们对正常的生理性肾功能以及病理过程机制的理解。     

Determination of post-translational modifications of proteins by high-sensitivity, high-resolution Fourier transform ion cyclotron resonance mass spectrometry

The response of a cell to its extracellular environment is a multi-step process beginning with signal transduction that is governed by "subtle changes" often resulting in protein expression. Proteomics is the tracking of this protein expression. Post-translational modification (PTM) is a "subtle change" that has a major influence on signal transduction. Phosphorylation and glycosylation propagate signals by sequential, reversible modifications. High-sensitivity, high-resolution and multiple MS capabilities of Fourier transform ion cyclotron resonance mass spectrometry permit localization of the PTM(s) with electron-capture dissociation, and then structural determination of the PTM with infrared multiphoton dissociation.     

Analysis of caged xanthones from the resin of Garcinia hanburyi using ultra-performance liquid chromatography/electrospray ionization quadrupole time-of-flight tandem mass spectrometry

On-line ultra high-performance liquid chromatography (UHPLC) coupled with electrospray quadrupole time-of-flight tandem mass spectrometry (ESI-QTOF-MS/MS/MS) has been developed for the analysis of a series of caged xanthones in the resin of Garcinia hanburyi. The fragmentation of protonated molecular ions for 12 known cadged xanthones was carried out using low-energy collision-induced electrospray ionization tandem mass spectrometry. It was found that Retro-Diels-Alder rearrangement occurred in the CID processes and produced the characteristic fragment ions, which are especially valuable for the identification of this class of xanthones. The fragmentation differential between some cis-, trans-isomers was uncovered. Computation methods were utilized to rationalize the observed MS behaviors. On-line UHPLC-ESI-MS/MS/MS method has proved to be rapid and efficient in that within 6min, 15 caged scaffold xanthones, including three pairs of epimers and four pairs of isomers in gamboges, were effectively separated and identified. Among them, two known, namely isogambogenin (13) and isomorellinol (14) and one likely new caged Garcinia xanthones from the Garcinia hanburyi were tentatively characterized based on the tandem mass spectra of known ones.     

基于不同提取方法的水稻叶片蛋白质组的二维液相色谱分离及高分辨质谱分析

建立了酚法提取-二维液相色谱分离-高分辨质谱分析水稻叶片蛋白质组的方法。水稻叶片蛋白质经过酚法提取,酶解肽段脱盐后用离线反相-反相二维液相色谱分离,然后用线性离子阱/静电场轨道阱组合式高分辨质谱分析,共鉴定到2712种蛋白质。比较了液相色谱分离系统（一维液相色谱与二维液相色谱）和水稻叶片蛋白质提取方法（酚法、十二烷基硫酸钠法（SDS法）和三氯乙酸/丙酮法（TCA/丙酮法））对鉴定蛋白质数量的影响,结果表明：在二维液相色谱条件下,酚法、SDS法和TCA/丙酮法鉴定到的蛋白质数目为2712、2415和1914,分别是一维液相色谱条件下鉴定到的蛋白质数目的2.7、2.5和1.9倍。二维液相色谱条件下,酚法鉴定到的蛋白质数目比SDS法和TCA/丙酮法分别多297和798。与SDS法和TCA/丙酮法相比,酚法不但鉴定到的蛋白质数量多,而且能够鉴定到一些极端蛋白质,如酸性、碱性及高等电点的蛋白质。此外,对二维液相色谱条件下3种蛋白质提取方法提取到的蛋白质进行生物学功能分类,发现3种方法鉴定到的蛋白质的功能存在互补性,但酚法鉴定到的蛋白质功能种类最多。该法为水稻蛋白质组学研究提供了技术支撑,同时也为其他作物的蛋白质组学研究技术提供重要的借鉴。     

Characterization of N-palmitoylated human growth hormone by in situ liquid-liquid extraction and MALDI tandem mass spectrometry

Acylation is a common post-translational modification found in secreted proteins and membrane-associated proteins, including signal transducing and regulatory proteins. Acylation is also explored in the pharmaceutical and biotechnology industry to increase the stability and lifetime of protein-based products. The presence of acyl moieties in proteins and peptides affects the physico-chemical properties of these species, thereby modulating protein stability, function, localization and molecular interactions. Characterization of protein acylation is a challenging analytical task, which includes the precise definition of the acylation sites in proteins and determination of the identity and molecular heterogeneity of the acyl moiety at each individual site. In this study, we generated a chemically modified human growth hormone (hGH) by incorporation of a palmitoyl moiety on the N(epsilon) group of a lysine residue. Monoacylation of the hGH protein was confirmed by determination of the intact molecular weight by mass spectrometry. Detailed analysis of protein acylation was achieved by analysis of peptides derived from hGH by protease treatment. However, peptide mass mapping by MALDI MS using trypsin and AspN proteases and standard sample preparation methods did not reveal any palmitoylated peptides. In contrast, in situ liquid-liquid extraction (LLE) performed directly on the MALDI MS metal target enabled detection of acylated peptide candidates by MALDI MS and demonstrated that hGH was N-palmitoylated at multiple lysine residues. MALDI MS and MS/MS analysis of the modified peptides mapped the N-palmitoylation sites to Lys158, Lys172 and Lys140 or Lys145. This study demonstrates the utility of LLE/MALDI MS/MS for mapping and characterization of acylation sites in proteins and peptides and the importance of optimizing sample preparation methods for mass spectrometry-based determination of substoichiometric, multi-site protein modifications.     

液相色谱-质谱联用方法用于严重急性呼吸系统综合症冠状病毒结构蛋白质的研究

通过高效液相反相色谱、毛细管反相色谱-串联质谱联用方法对SARS病毒攻击细胞的研究,鉴定出了N、S和M3种SARS结构蛋白质,并准确测定了N蛋白质的分子量。由分子量结果和生物信息学推断的N蛋白质的理论分子量比较,可以确定N蛋白质不存在常见的磷酸化修饰和糖基化修饰或含量很低。进一步的研究表明：N蛋白质可能存在降解现象,其降解机理尚需探索。另外,通过对样品直接酶切后进行两维毛细管分离和串联质谱鉴定与对样品先进行分离,然后再进行毛细管反相分离-串联质谱鉴定方法比较,表明两种方法在蛋白质组学研究中各具优缺点,可根据不同目的选择使用。     

A Novel Two-Stage Tandem Mass Spectrometry Approach and Scoring Scheme for the Identification of O-GlcNAc Modified Peptides

The modification of serine and threonine residues in proteins by a single N-acetylglucosamine (O-GlcNAc) residue is an emerging post-translational modification (PTM) with broad biological implications. However, the systematic or large-scale analysis of this PTM is hampered by several factors, including low stoichiometry and the lability of the O-glycosidic bond during tandem mass spectrometry. Using a library of 72 synthetic glycopeptides, we developed a two-stage tandem MS approach consisting of pulsed Q dissociation (PQD) for O-GlcNAc peptide detection and electron transfer dissociation (ETD) for identification and site localization. Based on a set of O-GlcNAc specific fragment ions, we further developed a score (OScore) that discriminates O-GlcNAc peptide spectra from spectra of unmodified peptides with 95% sensitivity and >99% specificity. Integrating the OScore into the two-stage LC-MS/MS approach detected O-GlcNAc peptides in the low fmol range and at 10-fold better sensitivity than a single data-dependent ETD tandem MS experiment.     

A robust two-dimensional separation for top-down tandem mass spectrometry of the low-mass proteome

For fractionation of intact proteins by molecular weight (MW), a sharply improved two-dimensional (2D) separation is presented to drive reproducible and robust fractionation before top-down mass spectrometry of complex mixtures. The “GELFrEE” (i.e., gel-eluted liquid fraction entrapment electrophoresis) approach is implemented by use of Tris-glycine and Tris-tricine gel systems applied to human cytosolic and nuclear extracts from HeLa S3 cells, to achieve a MW-based fractionation of proteins from 5 to >100 kDa in 1 h. For top-down tandem mass spectroscopy (MS/MS) of the low-mass proteome (5–25 kDa), between 5 and 8 gel-elution (GE) fractions are sampled by nanocapillary-LC-MS/MS with 12 or 14.5 tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers. Single injections give about 40 detectable proteins, about half of which yield automated ProSight identifications. Reproducibility metrics of the system are presented, along with comparative analysis of protein targets in mitotic versus asynchronous cells. We forward this basic 2D approach to facilitate wider implementation of top-down mass spectrometry and a variety of other protein separation and/or characterization approaches.