Protein identification using sequential ion/ion reactions and tandem mass spectrometry

Mass spectrometric analysis of body fluids for biomarker discovery

Hinging on the concept that extracellular proteins and polypeptides will provide information on the physiological state of specific organs, or even entire organisms, proteomic analysis of biological fluids for biomarker discovery has seen rapid expansion in recent years. Although multiple studies have had success using mass spectrometric analytical techniques for determination of proteins within a sample, inspection of naturally occurring species has been difficult, with most analyses using bottom-up methodology. We have applied a new fragmentation method, electron transfer dissociation (ETD), to this problem. We have previously illustrated the benefits to spectral quality and total identifications when using a combination of the complementary fragmentation techniques, ETD, and collision-activated dissociation, for analysis of naturally occurring proteins and polypeptides within biological fluids.

Identification and quantification of protein posttranslational modifications

Posttranslational modifications (PTMs) of proteins perform crucial roles in regulating the biology of the cell. PTMs are enzymatic, covalent chemical modifications of proteins that typically occur after the translation of mRNAs. These modifications are relevant because they can potentially change a protein's physical or chemical properties, activity, localization, or stability. Some PTMs can be added and removed dynamically as a mechanism for reversibly controlling protein function and cell signaling. Extensive investigations have aimed to identify PTMs and characterize their biological functions. This chapter will discuss the existing and emerging techniques in the field of mass spectrometry and proteomics that are available to identify and quantify PTMs. We will focus on the most frequently studied modifications. In addition, we will include an overview of the available tools and technologies in tandem mass spectrometry instrumentation that affect the ability to identify specific PTMs.

Peptide and protein ion/ion reactions in electrodynamic ion traps: tools and methods

Gas-phase reactions of oppositely charged ions can play important roles in the analysis of peptides and proteins. Electrospray ionization (ESI) can yield multiply charged versions of gaseous peptide and protein ions that can react with oppositely charged ions via several distinct mechanisms. Reagent ions that react via proton transfer can be used to facilitate protein mixture analysis and the mass assignment of product ions in a tandem mass spectrometry experiment. Proton transfer reactions can also be used to concentrate protein ion signals into one or two charge states and can be used to charge state purify a precursor ion population for subsequent dissociation. Electron transfer reactions have been shown to lead to fragmentation of gaseous protonated peptides and proteins. The extent of sequence information available from an electron transfer reaction is often greater than that obtained via conventional collision-induced dissociation. Electron transfer dissociation is particularly useful in probing the structures of polypeptides with labile posttranslational modifications. We summarize here the tools and general methods for conducting ion/ion reaction studies with emphasis on electrodynamic ion traps as the reaction vessels.

Electron capture dissociation of peptide hormone changes upon opening of the tocin ring and complexation with transition metal cations

Electron capture dissociation (ECD) is an analytical technique in mass spectrometry (MS) that allows detailed structural study of biomolecules to gain insight in their function. In this work the ECD behavior of two peptide hormones oxytocin (OT1) and vasopressin (VP1) was studied. The results of OT1 and VP1 were compared to structural analogues OT2 and VP2, which have similar amino acid sequences but lack the tocin ring. The ECD results showed that both the fragment type (c/z versus b/y) and the cleavage sites (ring versus tail) changed upon opening of the tocin ring. All four peptides were complexed with three different transition metal cations (Zn(2+), Ni(2+) and Cu(2+)) and the ECD results were compared to those obtained from the doubly protonated species. The use of various metal ions yielded different cleavages sites within the same peptide. This can be an effect of the metal ion itself, or a consequence of a change in conformation as was suggested earlier. In addition, the type of fragment ion varied for each metal-complexed peptide, which is in agreement with previous observations.

Sensitive and specific identification of wild type and variant proteins from 8 to 669 kDa using top-down mass spectrometry

Top-down and bottom-up mass spectrometry methods can generate gas phase fragments and use these to identify proteins. Top-down methods, in addition, can provide the mass of the protein itself and therefore additional structural information. Despite the conceptual advantage of top-down methods, the market share advantage belongs to bottom-up methods as a result of their more robust sample preparation, fragmentation, and data processing methods. Here we report improved fragmentation and data processing methods for top-down mass spectrometry. Specifically we report the use of funnel-skimmer dissociation, a variation of nozzle-skimmer dissociation, and compare its performance with electron capture dissociation. We also debut BIG Mascot, an extended version of Mascot with incorporated top-down MS(2) search ability and the first search engine that can perform both bottom-up and top-down searches. Using BIG Mascot, we demonstrated the ability to identify proteins 1) using only intact protein MS(1), 2) using only MS(2), and 3) using the combination of MS(1) and MS(2). We correctly identified proteins with a wide range of masses, including 13 amyotrophic lateral sclerosis-associated variants of the protein Cu/Zn-superoxide dismutase, and extended the upper mass limit of top-down protein identification to 669 kDa by identifying thyroglobulin.

Atmospheric pressure thermal dissociation of phospho- and sulfopeptides

Several phospho- and sulfopeptides were subjected to atmospheric pressure thermal dissociation (APTD), which was effected by passing peptide ions generated by electrosonic spray ionization (ESSI) through a heated coiled metal tube. Sequence informative fragment ions including a-, b-, c-, and y-types of ions were observed with increased relative intensities under APTD compared with collision-induced dissociation (CID), performed inside the ion trap. A certain degree of preservation of phosphate and sulfate ester moieties was observed for some fragments ions under APTD. The neutral fragments generated outside the mass spectrometer were further analyzed via on-line corona discharge to provide rich and complementary sequence information to that provided by the fragment ions directly obtained from APTD, although complete losses of the modification groups were noted. Improved primary sequence information for phospho- and sulfopeptides was typically obtained by analyzing both ionic and neutral fragments from APTD compared with fragment ions from CID alone. Localization of the modification sites of phospho- and sulfopeptides was achieved by combining the structural information acquired from APTD and CID.

Multidimensional LC separations in shotgun proteomics

Two modes of separation coupled with MS enable researchers to study complicated biological structures.

Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation

Chromatin undergoes developmentally-regulated structural and chemical changes as cells differentiate, which subsequently lead to differences in cellular function by altering patterns of gene expression. To gain insight into chromatin alterations that occur during mammalian differentiation, we turned to a mouse embryonic stem cell (ESC) model. Here we show that histone H3 is proteolytically cleaved at its N-terminus during ESC differentiation. We map the sites of H3 cleavage and identify Cathepsin L as a protease responsible for proteolytically processing the N-terminal H3 tail. In addition, our data suggest that H3 cleavage may be regulated by covalent modifications present on the histone tail itself. Our studies underscore the intriguing possibility that histone proteolysis, brought about by Cathepsin L and potentially other family members, plays a role in development and differentiation that was not previously recognized.

Mass spectrometry in systems biology: an overview

As an emerging field, systems biology is currently the talk of the town, which challenges our philosophy in comprehending biology. Instead of the reduction approach advocated in molecular biology, systems biology aims at systems-level understanding of correlations among molecular components. Such comprehensive investigation requires massive information from the "omics" cascade demanding high-throughput screening techniques. Being one of the most versatile analytical methods, mass spectrometry has already been playing a significant role at this early stage of systems biology. In this review, we documented the advances in modern mass spectrometry technologies as well as nascent inventions. Recent applications of mass spectrometry-based techniques and methodologies in genomics, proteomics, transcriptomics and metabolomics will be further elaborated individually. Undoubtedly, more applications of mass spectrometry in systems biology can be expected in the near future.

Mass spectrometry in biodefense

Potential agents for biological attacks include both microorganisms and toxins. In mass spectrometry (MS), rapid identification of potential bioagents is achieved by detecting the masses of unique biomarkers, correlated to each agent. Currently, proteins are the most reliable biomarkers for detection and characterization of both microorganisms and toxins, and MS-based proteomics is particularly well suited for biodefense applications. Confident identification of an organism can be achieved by top-down proteomics following identification of individual protein biomarkers from their tandem mass spectra. In bottom-up proteomics, rapid digestion of intact protein biomarkers is again followed by MS/MS to provide unambiguous bioagent identification and characterization. Bioinformatics obviates the need for culturing and rigorous control of experimental variables to create and use MS fingerprint libraries for various classes of bioweapons. For specific applications, MS methods, instruments and algorithms have also been developed for identification based on biomarkers other than proteins and peptides.

Orbitrap mass spectrometry: instrumentation, ion motion and applications

Since its introduction, the orbitrap has proven to be a robust mass analyzer that can routinely deliver high resolving power and mass accuracy. Unlike conventional ion traps such as the Paul and Penning traps, the orbitrap uses only electrostatic fields to confine and to analyze injected ion populations. In addition, its relatively low cost, simple design and high space-charge capacity make it suitable for tackling complex scientific problems in which high performance is required. This review begins with a brief account of the set of inventions that led to the orbitrap, followed by a qualitative description of ion capture, ion motion in the trap and modes of detection. Various orbitrap instruments, including the commercially available linear ion trap-orbitrap hybrid mass spectrometers, are also discussed with emphasis on the different methods used to inject ions into the trap. Figures of merit such as resolving power, mass accuracy, dynamic range and sensitivity of each type of instrument are compared. In addition, experimental techniques that allow mass-selective manipulation of the motion of confined ions and their potential application in tandem mass spectrometry in the orbitrap are described. Finally, some specific applications are reviewed to illustrate the performance and versatility of the orbitrap mass spectrometers.

Analysis of histones in Xenopus laevis. II. mass spectrometry reveals an index of cell type-specific modifications on H3 and H4

Epigenetic information is hypothesized to be encoded in histone variants and post-translational modifications. Varied cell- and locus-specific combinations of these epigenetic marks are likely contributors to regulation of chromatin-templated transactions, including transcription, replication, recombination, and repair. Therefore, the relative abundance of histone modifications in a given cell type is a potential index of cell fate and specificity. Here, we utilize mass spectrometry techniques to characterize the relative abundance index of cell type-specific modifications on histones H3 and H4 in distinct cell types from the frog Xenopus laevis, including the sperm, the stored predeposition histones in the egg, the early embryo equivalent pronuclei, cultured somatic cells, and erythrocytes. We used collisionally associated dissociation to identify the modifications present on histone H3 in a variety of cell types, resolving 26 distinctly modified H3 peptides. We employed the electron transfer dissociation fragmentation technique in a "middle-down" approach on the H4 N-terminal tail to explore the overlap of post-translational modifications. We observed 66 discrete isoforms of the H4 1-23 fragment in four different cell types. Isolation of the stored, predeposition histone H4 from the frog egg also revealed a more varied pattern of modifications than the previously known diacetylation on Lys(5) and Lys(12). The developmental transitions of modifications on H3 and H4 were strikingly varied, implying a strong correlation of the histone code with cell type and fate. Our results are consistent with a histone code index for each cell type and uncover potential cross-talk between modifications on a single tail.

Decision tree-driven tandem mass spectrometry for shotgun proteomics

Mass spectrometry has become a key technology for modern large-scale protein sequencing. Tandem mass spectrometry, the process of peptide ion dissociation followed by mass-to-charge ratio (m/z) analysis, is the critical component for peptide identification. Recent advances in mass spectrometry now permit two discrete, and complementary, types of peptide ion fragmentation: collision-activated dissociation (CAD) and electron transfer dissociation (ETD) on a single instrument. To exploit this complementarity and increase sequencing success rates, we designed and embedded a data-dependent decision tree algorithm (DT) to make unsupervised, real-time decisions of which fragmentation method to use based on precursor charge and m/z. Applying the DT to large-scale proteome analyses of Saccharomyces cerevisiae and human embryonic stem cells, we identified 53,055 peptides in total, which was greater than by using CAD (38,293) or ETD (39,507) alone. In addition, the DT method also identified 7,422 phosphopeptides, compared to either 2,801 (CAD) or 5,874 (ETD) phosphopeptides.

In vacuo formation of peptide-metal coordination complexes

Here we report on the reaction of rhenate anions (ReO(3) (-)) with multiply protonated peptide cations in a quadrupole linear ion trap mass spectrometer. These reactions effect the formation of an anion-cation complex that, upon collisional activation, dissociates along the peptide backbone rather than by displacement of the anion. Cleavage of the peptide backbone, with anion retention, leads us to conclude the anion-cationcomplexmust be tightly bound, most probably through coordination chemistry. We describe this chemistry and detail the possible application of such ion attachment reactions to the characterization of intact proteins.

Ion-Ion Reactions with Fixed-Charge Modified Proteins to Produce Ions in a Single, Very High Charge State

Electrospray ionization (ESI) of denatured proteins produces a mass spectrum with a broad distribution of multiply charged ions. Attaching fixed positive charges, specifically quaternary ammonium groups, to proteins at their carboxylic acid groups generates substantially higher charge states compared to the corresponding unmodified proteins in positive-mode ESI. Ion-ion reactions of these modified proteins with reagent anions leads to charge reduction by proton transfer. These proton transfer reactions cannot remove charge from the quaternary ammonium groups, which do not have a proton to transfer to the anion. Thus, one might expect charge reduction to stop at a single charge state equal to the number of fixed charges on the modified protein. However, ion-ion reactions yield charge states lower than this number of fixed charges due to anion attachment (adduction) to the proteins. Charge reduction via ion-molecule reactions involving gas-phase bases also give adducts on the modified protein ions in low charge states. Such adducts are avoided by keeping the ions in charge states well above the number of fixed charges. In the present work protein ions were selectively "parked" within an ion trap mass spectrometer in a high charge state by mild radiofrequency excitation that dramatically slows their ion-ion reaction rate-a technique termed "ion parking". The combination of ion parking with the fixed-charge modified proteins permits generation of a large population of ions in a single, very high charge state.

Mass spectrometry and the emerging field of glycomics

The biological significance of protein and lipid glycosylation is well established. For example, cells respond to environmental stimuli by altering glycan structures on their surfaces, and cancer cells evade normal growth regulation in part by remodeling their surface glycans. In general, glycan chemical properties differ significantly from those of proteins, lipids, nucleic acids, and small molecule metabolites. Thus, advances in glycomics, a comprehensive study to identify all glycans in an organism, rely on the development of specialized analytical methods. Mass spectrometry (MS) is emerging as an enabling technology in the field of glycomics. This review summarizes recent developments in mass spectrometric analysis methods for protein-based glycomics and glycoproteomics workflows.

Modification of Pseudomonas aeruginosa Pa5196 type IV Pilins at multiple sites with D-Araf by a novel GT-C family Arabinosyltransferase, TfpW

Pseudomonas aeruginosa Pa5196 produces type IV pilins modified with unusual alpha1,5-linked d-arabinofuranose (alpha1,5-D-Araf) glycans, identical to those in the lipoarabinomannan and arabinogalactan cell wall polymers from Mycobacterium spp. In this work, we identify a second strain of P. aeruginosa, PA7, capable of expressing arabinosylated pilins and use a combination of site-directed mutagenesis, electrospray ionization mass spectrometry (MS), and electron transfer dissociation MS to identify the exact sites and extent of pilin modification in strain Pa5196. Unlike previously characterized type IV pilins that are glycosylated at a single position, those from strain Pa5196 were modified at multiple sites, with modifications of alphabeta-loop residues Thr64 and Thr66 being important for normal pilus assembly. Trisaccharides of alpha1,5-D-Araf were the principal modifications at Thr64 and Thr66, with additional mono- and disaccharides identified on Ser residues within the antiparallel beta sheet region of the pilin. TfpW was hypothesized to encode the pilin glycosyltransferase based on its genetic linkage to the pilin, weak similarity to membrane-bound GT-C family glycosyltransferases (which include the Mycobacterium arabinosyltransferases EmbA/B/C), and the presence of characteristic motifs. Loss of TfpW or mutation of key residues within the signature GT-C glycosyltransferase motif completely abrogated pilin glycosylation, confirming its involvement in this process. A Pa5196 pilA mutant complemented with other Pseudomonas pilins containing potential sites of modification expressed nonglycosylated pilins, showing that TfpW's pilin substrate specificity is restricted. TfpW is the prototype of a new type IV pilin posttranslational modification system and the first reported gram-negative member of the GT-C glycosyltransferase family.

Unraveling the histone's potential: a proteomics perspective

Post translational modification (PTM) of histones has long been associated with epigenetic regulation. Although genomic approaches have established correlation between a handful of histone PTMs and transcriptional states, only recently have advancements in proteomics provided the tools necessary to study histone proteins and their relevant modifications in this context. Using mass spectrometry, researchers have demonstrated the ability to determine the full repertoire of histone PTMs, their residue specific location, the combinations in which they exist, and the proteins that interact with these combinations. Moving forward it will be imperative to develop novel approaches that combine proteomic and genomic technologies to determine the functional significance of these combinations of modifications. Assays with increased specificity will resolve more focused biological questions and determine to what extent, and by what mechanisms, histones influence transcription.

Stable high volumetric production of glycosylated human recombinant IFNalpha2b in HEK293 cells

Background

Mammalian cells are becoming the prevailing expression system for the production of recombinant proteins because of their capacity for proper protein folding, assembly, and post-translational modifications. These systems currently allow high volumetric production of monoclonal recombinant antibodies in the range of grams per litre. However their use for large-scale expression of cytokines typically results in much lower volumetric productivity.

Results

We have engineered a HEK293 cell clone for high level production of human recombinant glycosylated IFNα2b and developed a rapid and efficient method for its purification. This clone steadily produces more than 200 mg (up to 333 mg) of human recombinant IFNα2b per liter of serum-free culture, which can be purified by a single-step cation-exchange chromatography following media acidification and clarification. This rapid procedure yields 98% pure IFNα2b with a recovery greater than 70%. Purified IFNα2b migrates on SDS-PAGE as two species, a major 21 kDa band and a minor 19 kDa band. N-terminal sequences of both forms are identical and correspond to the expected mature protein. Purified IFNα2b elutes at neutral pH as a single peak with an apparent molecular weight of 44,000 Da as determined by size-exclusion chromatography. The presence of intramolecular and absence of intermolecular disulfide bridges is evidenced by the fact that non-reduced IFNα2b has a greater electrophoretic mobility than the reduced form. Treatment of purified IFNα2b with neuraminidase followed by O-glycosidase both increases electrophoretic mobility, indicating the presence of sialylated O-linked glycan. A detailed analysis of glycosylation by mass spectroscopy identifies disialylated and monosialylated forms as the major constituents of purified IFNα2b. Electron transfer dissociation (ETD) shows that the glycans are linked to the expected threonine at position 106. Other minor glycosylated forms and non-sialylated species are also detected, similar to IFNα2b produced naturally by lymphocytes. Further, the HEK293-produced IFNα2b is biologically active as shown with reporter gene and antiviral assays.

Conclusion

These results show that the HEK293 cell line is an efficient and valuable host for the production of biologically active and glycosylated human IFNα2b.

Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics

Proteomics experiments on complex mixtures have benefited greatly from the advent of fast-scanning ion trap mass spectrometers. However, the complexity and dynamic range of mixtures analyzed using shotgun proteomics is still beyond what can be sampled by data-dependent acquisition. Furthermore, the total liquid chromatography-mass spectrometry (LC-MS) peak capacity is not sufficient to resolve the precursors within these mixtures, let alone acquire tandem mass spectra on all of them. Here we describe the application of a high-field asymmetric waveform ion mobility spectrometry (FAIMS) device as an interface to an ion trap mass spectrometer. The dynamic range and peak capacity of the nanoflow LC-FAIMS-MS analysis was assessed using a complex tryptic digest of S. cerevisiae proteins. By adding this relatively simple device to the front of the mass spectrometer, we obtain an increase in peak capacity >8-fold and an increase in dynamic range of >5-fold, without increasing the length of the LC-MS analysis. Thus, the addition of FAIMS to the front of a table-top mass spectrometer can obtain the peak capacity of multidimensional protein identification technology (MudPIT) while increasing the throughput by a factor of 12.

A combinatorial H4 tail library for exploring the histone code

Histone modifications modulate chromatin structure and function. A posttranslational modification-randomized, combinatorial library based on the first 21 residues of histone H4 was designed for systematic examination of proteins that interpret a histone code. The 800-member library represented all permutations of most known modifications within the N-terminal tail of histone H4. To determine its utility in a protein binding assay, the on-bead library was screened with an antibody directed against phosphoserine 1 of H4. Among the hits, 59 of 60 sequences were phosphorylated at S1, while 30 of 30 of those selected from the nonhits were unphosphorylated. A 512-member version of the library was then used to determine the binding specificity of the double tudor domain of hJMJD2A, a histone demethylase involved in transcriptional repression. Global linear least-squares fitting of modifications from the identified peptides (40 hits and 34 nonhits) indicated that methylation of K20 was the primary determinant for binding, but that phosphorylation and acetylation of neighboring sites attenuated the interaction. To validate the on-bead screen, isothermal titration calorimetry was performed with 13 H4 peptides. Dissociation constants ranged from 1 mM to 1 microM and corroborated the screening results. The general approach should be useful for probing the specificity of any histone-binding protein.

Top-down identification and characterization of biomolecules by mass spectrometry

The most widely used modern mass spectrometers face severe performance limitations with molecules larger than a few kDa. For far larger biomolecules, a common practice has been to break these up chemically or enzymatically into fragments that are sufficiently small for the instrumentation available. With its many sophisticated recent enhancements, this "bottom-up" approach has proved highly valuable, such as for the rapid, routine identification and quantitation of DNA-predicted proteins in complex mixtures. Characterization of smaller molecules, however, has always measured the mass of the molecule and then that of its fragments. This "top-down" approach has been made possible for direct analysis of large biomolecules by the uniquely high (>10(5)) mass resolving power and accuracy ( approximately 1 ppm) of the Fourier-transform mass spectrometer. For complex mixtures, isolation of a single component's molecular ions for MS/MS not only gives biomolecule identifications of far higher reliability, but directly characterizes sequence errors and post-translational modifications. Protein sizes amenable for current MS/MS instrumentation are increased by a "middle-down" approach in which limited proteolysis forms large (e.g., 10 kDa) polypeptides that are then subjected to the top-down approach, or by "prefolding dissociation." The latter, which extends characterization to proteins >200 kDa, was made possible by greater understanding of how molecular ion tertiary structure evolves in the gas phase.

A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer

Here we detail the modification of a quadrupole linear ion trap-orbitrap hybrid (QLT-orbitrap) mass spectrometer to accommodate a negative chemical ionization (NCI) source. The NCI source is used to produce fluoranthene radical anions for imparting electron transfer dissociation (ETD). The anion beam is stable, robust, and intense so that a sufficient amount of reagents can be injected into the QLT in only 4-8 ms. Following ion/ion reaction in the QLT, ETD product ions are mass-to-charge (m/z) analyzed in either the QLT (for speed and sensitivity) or the orbitrap (for mass resolution and accuracy). Here we describe the physical layout of this device, parametric optimization of anion transport, an evaluation of relevant ETD figures of merit, and the application of this instrument to protein sequence analysis. Described proteomic applications include complex peptide mixture analysis, post-translational modification (PTM) site identification, isotope-encoded quantitation, large peptide characterization, and intact protein analysis. From these experiments, we conclude the ETD-enabled orbitrap will provide the proteomic field with several new opportunities and represents an advance in protein sequence analysis technologies.

Comprehensive comparison of collision induced dissociation and electron transfer dissociation

Electron transfer dissociation (ETD) is a recently introduced mass spectrometric technique which has proven to be an excellent tool for the elucidation of labile post-translational modifications such as phosphorylation and O-GlcNAcylation of serine and threonine residues. However, unlike collision induced dissociation (CID), which has been studied for decades, the intricacies of ETD-based fragmentation have not yet been firmly established or systematically addressed. In this analysis, we have systematically compared the CID and ETD fragmentation patterns for the large majority of the peptides that do not contain such labile modifications. Using a standard 48 protein mix, we were able to measure false-positive rates for the experiments and also assess a large number of peptides for a detailed comparison of CID and ETD fragmentation pattern. Analysis of approximately 19,000 peptides derived from both standard proteins and complex protein samples revealed that (i) CID identified 50% more peptides than ETD; (ii) ETD resulted in approximately 20% increase in amino acid sequence coverage over CID; and (iii) combining CID and ETD fragmentation increased the sequence coverage for an average tryptic peptide to 92%. Interestingly, our analysis revealed that nearly 60% of all ETD-identified peptides carried two positive charges, which is in sharp contrast to what has been generally accepted. We also present a novel strategy for automatic validation of peptide assignments based on identification of a peptide by consecutive CID and ETD fragmentation in an alternating mode.

Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells

Epigenetic regulation through chromatin is thought to play a critical role in the establishment and maintenance of pluripotency. Traditionally, antibody-based technologies were used to probe for specific posttranslational modifications (PTMs) present on histone tails, but these methods do not generally reveal the presence of multiple modifications on a single-histone tail (combinatorial codes). Here, we describe technology for the discovery and quantification of histone combinatorial codes that is based on chromatography and mass spectrometry. We applied this methodology to decipher 74 discrete combinatorial codes on the tail of histone H4 from human embryonic stem (ES) cells. Finally, we quantified the abundances of these codes as human ES cells undergo differentiation to reveal striking changes in methylation and acetylation patterns. For example, H4R3 methylation was observed only in the presence of H4K20 dimethylation; such context-specific patterning exemplifies the power of this technique.

Hydrophilic interaction liquid chromatography (HILIC) in proteomics

In proteomics, nanoflow multidimensional chromatography is now the gold standard for the separation of complex mixtures of peptides as generated by in-solution digestion of whole-cell lysates. Ideally, the different stationary phases used in multidimensional chromatography should provide orthogonal separation characteristics. For this reason, the combination of strong cation exchange chromatography (SCX) and reversed-phase (RP) chromatography is the most widely used combination for the separation of peptides. Here, we review the potential of hydrophilic interaction liquid chromatography (HILIC) as a separation tool in the multidimensional separation of peptides in proteomics applications. Recent work has revealed that HILIC may provide an excellent alternative to SCX, possessing several advantages in the area of separation power and targeted analysis of protein post-translational modifications. [figure: see text]

Evolution of instrumentation for the study of gas-phase ion/ion chemistry via mass spectrometry

The scope of gas-phase ion/ion chemistry accessible to mass spectrometry is largely defined by the available tools. Due to the development of novel instrumentation, a wide range of reaction phenomenologies has been noted, many of which have been studied extensively and exploited for analytical applications. This perspective presents the development of mass spectrometry-based instrumentation for the study of the gas-phase ion/ion chemistry in which at least one of the reactants is multiply charged. The instrument evolution is presented within the context of three essential elements required for any ion/ion reaction study: the ionization source(s), the reaction vessel or environment, and the mass analyzer. Ionization source arrangements have included source combinations that allow for reactions between multiply charged ions of one polarity and singly charged ions of opposite polarity, arrangements that enable the study of reactions of multiply charged ions of opposite polarity and, most recently, arrangements that allow for ion formation from more than two ion sources. Gas-phase ion/ion reaction studies have been performed at near atmospheric pressure in flow reactor designs and within electrodynamic ion traps operated in the mTorr range. With ion trap as a reaction vessel, ionization and reaction processes can be independently optimized and ion/ion reactions can be implemented within the context of MSn experiments. Spatial separation of the reaction vessel from the mass analyzer allows for the use of any form of mass analysis in conjunction with ion/ion reactions. Time-of-flight mass analysis, for example, has provided significant improvements in mass analysis figures of merit relative to mass filters and ion traps.

Fragmentation of multiply-charged intact protein ions using MALDI TOF-TOF mass spectrometry

Top down proteomics in a TOF-TOF instrument was further explored by examining the fragmentation of multiply charged precursors ions generated by matrix-assisted laser desorption ionization. Evaluation of sample preparation conditions allowed selection of solvent/matrix conditions and sample deposition methods to produce sufficiently abundant doubly and triply charged precursor ions for subsequent CID experiments. As previously reported, preferential cleavage was observed at sites C-terminal to acidic residues and N-terminal to proline residues for all ions examined. An increase in nonpreferential fragmentation as well as additional low mass product ions was observed in the spectra from multiply charged precursor ions providing increased sequence coverage. This enhanced fragmentation from multiply charged precursor ions became increasingly important with increasing protein molecular weight and facilitates protein identification using database searching algorithms. The useable mass range for MALDI TOF-TOF analysis of intact proteins has been expanded to 18.2 kDa using this approach.

Online microwave D-cleavage LC-ESI-MS/MS of intact proteins: site-specific cleavages at aspartic acid residues and disulfide bonds

An online nonenzymatic digestion method utilizing a microwave-heated flow cell and mild acid hydrolysis at aspartic acid (D) for rapid protein identification is described. This methodology, here termed microwave D-cleavage, was tested with proteins ranging in size from 5 kDa (insulin) to 67 kDa (bovine serum albumin) and a bacterial cell lysate ( Escherichia coli). A microwave flow cell consisting of a 5 microL total volume reaction loop connected to a sealed reaction vessel was introduced into a research grade microwave oven. With this dynamic arrangement, the injected sample was subjected to microwave radiation as it flowed through the reaction loop and was digested in less than 5 min. Different digestion times can be achieved by varying the sample flow rate and/or length of the loop inside the microwave flow cell. The microwave flow cell can be operated individually with the output being collected for matrix assisted laser ionization/desorption (MALDI) mass spectrometry (MS) or connected online for liquid chromatography (LC) electrospray ionization (ESI)-MS. In the latter configuration, the microwave flow cell eluates containing digestion products were transferred online to a reversed phase liquid chromatography column for direct ESI-MS and ESI-MS/MS analyses (specifically, Collision Induced Dissociation, CID). Concurrently with the microwave D-cleavage step, disulfide bond reduction/cleavage was achieved by the coinjection of dithiothreitol (DTT) with the sample prior to online microwave heating and online LC-MS analysis and so eliminating the need for alkylation of the reduced protein. All protein standards, protein mixtures, and proteins in a bacterial cell lysate analyzed by this new online methodology were successfully identified via a SEQUEST database search of fragment ion mass spectra. Overall, online protein digestion and identification was achieved in less than 40 min total analysis time, including the chromatographic step.

Challenges of using mass spectrometry as a bladder cancer biomarker discovery platform

INTRODUCTION

Bladder cancer (BCa) is one of the most prevalent malignancies worldwide, mostly due to its high recurrence rates. In consequence, the necessity of repeated screening for reappearance demonstrates the urgent need for novel biomarkers as alternatives to invasive standard procedures.

METHODS

Proteomic technologies have emerged as powerful platforms for unbiased biomarker discovery and revolutionized the classical "target-driven" analysis of single marker candidates. Although proteome profiling is still far from demonstrating its full potential in clinical diagnosis, first studies clearly denote its significant potential.

CONCLUSIONS

This review provides a discussion of the challenges related to clinical proteomics using mass spectrometry, emphasizing bladder cancer biomarker discovery. An outline of the technological prerequisites for reliable proteome profiling, data mining and interpretation, as well as, reflections on future trends in the field are provided.

Methods for analyzing peptides and proteins on a chromatographic timescale by electron-transfer dissociation mass spectrometry

Advancement in proteomics research relies on the development of new, innovative tools for identifying and characterizing proteins. Here, we describe a protocol for analyzing peptides and proteins on a chromatographic timescale by coupling nanoflow reverse-phase (RP) liquid chromatography (LC) to electron-transfer dissociation (ETD) mass spectrometry. For this protocol, proteins can be proteolytically digested before ETD analysis, although digestion is not necessary for all applications. Proteins Collapse

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MESH Headings

• Chromatography, Liquid/methods
• Ions/chemistry
• Mass Spectrometry/methods
• Peptides/chemistry
• Phosphorylation
• Proteins/chemistry
• Proteomics/methods
• rev Gene Products, Human Immunodeficiency Virus/chemistry

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Grants

• R01 GM037537 NIGMS NIH HHS
• R01 GM037537-23 NIGMS NIH HHS
• GM37537 NIGMS NIH HHS

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Affiliation(s)

Namrata D Udeshi University of Virginia, Department of Chemistry, McCormick Road, Charlottesville, Virginia 22904, USA
Philip D Compton
Jeffrey Shabanowitz
Donald F Hunt
Kristie L Rose

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Protein identification via ion-trap collision-induced dissociation and examination of low-mass product ions

A whole-protein tandem mass spectrometry approach for protein identification based on precursor ion charge state concentration via ion/ion reactions, ion-trap collisional activation, ion/ion proton-transfer reactions involving the product ions, and mass analysis over a narrow m/z range (up to m/z 2000) is described and evaluated. The experiments were carried out with a commercially available electrospray ion-trap instrument that has been modified to allow for ion/ion reactions. Reaction conditions and the approach to searching protein databases were developed with the assumption that the resolving power of the mass analyzer is insufficient to distinguish charge states on the basis of the isotope spacings. Ions derived from several charge states of cytochrome c, myoglobin, ribonuclease A, and ubiquitin were used to evaluate the approach for protein identification and to develop a two-step procedure to database searching to optimize specificity. The approach developed with the model proteins was then applied to whole cell lysate fractions of Saccharomyces cerevisiae. The results are illustrated with examples of assignments made for three a priori unknown proteins, each selected randomly from a lysate fraction. Two of the three proteins were assigned to species present in the database, whereas one did not match well any database entry. The combination of the mass measurement and the product ion masses suggested the possibility for the oxidation of two methionine residues of a protein in the database. The examples show that this limited whole-protein characterization approach can provide insights that might otherwise be lacking with approaches based on complete enzymatic digestion.

Electron transfer dissociation in the hexapole collision cell of a hybrid quadrupole-hexapole Fourier transform ion cyclotron resonance mass spectrometer

Electron transfer dissociation (ETD) of proteins is demonstrated in a hybrid quadrupole-hexapole Fourier transform ion cyclotron resonance mass spectrometer (Qh-FTICRMS). Analyte ions are selected in the mass analyzing quadrupole, accumulated in the hexapole linear ion trap, reacted with fluoranthene reagent anions, and then analyzed via an FTICR mass analyzer. The hexapole trap allows for a broad fragment ion mass range and a high ion storage capacity. Using a 3 T FTICRMS, resolutions of 60 000 were achieved with mass accuracies averaging below 1.4 ppm. The high resolution, high mass accuracy ETD spectra provided by FTICR obviates the need for proton transfer reaction (PTR) charge state reduction of ETD product ions when analyzing proteins or large peptides. This is demonstrated with the ETD of ubiquitin and apomyoglobin yielding sequence coverages of 37 and 20%, respectively. We believe this represents the first reported successful combination of ETD and a FTICRMS.

Decoding protein modifications using top-down mass spectrometry

Top-down mass spectrometry is an emerging technology which strives to preserve the post-translationally modified forms of proteins present in vivo by measuring them intact, rather than measuring peptides produced from them by proteolysis. The top-down technology is beginning to capture the interest of biologists and mass spectrometrists alike, with a main goal of deciphering interaction networks operative in cellular pathways. Here we outline recent approaches and applications of top-down mass spectrometry as well as an outlook for its future.

Analysis of proteins and peptides on a chromatographic timescale by electron-transfer dissociation MS

Peptide and protein sequence analysis using a combination of gas-phase ion-ion chemistry and tandem MS is described. Samples are converted to multiply charged ions by ESI and then allowed to react with fluoranthene radical anions in a quadrupole linear ion trap mass spectrometer. Electron transfer from the radical anion to the multiply charged peptide or protein promotes random fragmentation along the amide backbone that is independent of peptide or protein size, sequence, or the presence of post-translational modifications. Examples are provided that demonstrate the utility of electron-transfer dissociation for characterizing post-translational modifications and for identifying proteins in mixtures on a chromatographic timescale (500 ms/protein).

Top-down proteomics on a chromatographic time scale using linear ion trap fourier transform hybrid mass spectrometers

Proteomics has grown significantly with the aid of new technologies that consistently are becoming more streamlined. While processing of proteins from a whole cell lysate is typically done in a bottom-up fashion utilizing MS/MS of peptides from enzymatically digested proteins, top-down proteomics is becoming a viable alternative that until recently has been limited largely to offline analysis by tandem mass spectrometry. Here we describe a method for high-resolution tandem mass spectrometery of intact proteins on a chromatographic time scale. In a single liquid chromatography-tandem mass spectrometry (LC-MS/MS) run, we have identified 22 yeast proteins with molecular weights from 14 to 35 kDa. Using anion exchange chromatography to fractionate a whole cell lysate before online LC-MS/MS, we have detected 231 metabolically labeled (14N/15N) protein pairs from Saccharomyces cerevisiae. Thirty-nine additional proteins were identified and characterized from LC-MS/MS of selected anion exchange fractions. Automated localization of multiple acetylations on Histone H4 was also accomplished on an LC time scale from a complex protein mixture. To our knowledge, this is the first demonstration of top-down proteomics (i.e., many identifications) on linear ion trap Fourier transform (LTQ FT) systems using high-resolution MS/MS data obtained on a chromatographic time scale.

Performance Characteristics of Electron Transfer Dissociation Mass Spectrometry

We performed a large scale study of electron transfer dissociation (ETD) performance, as compared with ion trap collision-activated dissociation (CAD), for peptides ranging from approximately 1000 to 5000 Da (n approximately 4000). These data indicate relatively little overlap in peptide identifications between the two methods ( approximately 12%). ETD outperformed CAD for all charge states greater than 2; however, regardless of precursor charge a linear decrease in percent fragmentation, as a function of increasing precursor m/z, was observed with ETD fragmentation. We postulate that several precursor cation attributes, including peptide length, charge distribution, and total mass, could be relevant players. To examine these parameters unique ETD-identified peptides were sorted by length, and the ratio of amino acid residues per precursor charge (residues/charge) was calculated. We observed excellent correlation between the ratio of residues/charge and percent fragmentation. For peptides of a given residue/charge ratio, there is no correlation between peptide mass and percent fragmentation; instead we conclude that the ratio of residues/charge is the main factor in determining a successful ETD outcome. As charge density decreases so does the probability of non-covalent interactions that can bind a newly formed c/z-type ion pair. Recently we have described a supplemental activation approach (ETcaD) to convert these non-dissociative electron transfer product ions to useful c- and z-type ions. Automated implementation of such methods should remove this apparent precursor m/z ceiling. Finally, we evaluated the role of ion density (both anionic and cationic) and reaction duration for an ETD experiment. These data indicate that the best performance is achieved when the ion trap is filled to its space charge limit with anionic reagents. In this largest scale study of ETD to date, ETD continues to show great promise to propel the field of proteomics and, for small- to medium-sized peptides, is highly complementary to ion trap CAD.

Tandem phosphorylation of Ser-911 and Thr-912 at the C terminus of yeast plasma membrane H+-ATPase leads to glucose-dependent activation

In recent years there has been growing interest in the post-translational regulation of P-type ATPases by protein kinase-mediated phosphorylation. Pma1 H(+)-ATPase, which is responsible for H(+)-dependent nutrient uptake in yeast (Saccharomyces cerevisiae), is one such example, displaying a rapid 5-10-fold increase in activity when carbon-starved cells are exposed to glucose. Activation has been linked to Ser/Thr phosphorylation in the C-terminal tail of the ATPase, but the specific phosphorylation sites have not previously been mapped. The present study has used nanoflow high pressure liquid chromatography coupled with electrospray electron transfer dissociation tandem mass spectrometry to identify Ser-911 and Thr-912 as two major phosphorylation sites that are clearly related to glucose activation. In carbon-starved cells with low Pma1 activity, peptide 896-918, which was derived from the C terminus upon Lys-C proteolysis, was found to be singly phosphorylated at Thr-912, whereas in glucose-metabolizing cells with high ATPase activity, the same peptide was doubly phosphorylated at Ser-911 and Thr-912. Reciprocal (14)N/(15)N metabolic labeling of cells was used to measure the relative phosphorylation levels at the two sites. The addition of glucose to carbon-starved cells led to a 3-fold reduction in the singly phosphorylated form and an 11-fold increase in the doubly phosphorylated form. These results point to a mechanism in which the stepwise phosphorylation of two tandemly positioned residues near the C terminus mediates glucose-dependent activation of the H(+)-ATPase.

Electron transfer dissociation of doubly sodiated glycerophosphocholine lipids

The ability to generate gaseous doubly charged cations of glycerophosphocholine (GPC) lipids via electrospray ionization has made possible the evaluation of electron-transfer dissociation (ETD) for their structural characterization. Doubly sodiated GPC cations have been reacted with azobenzene radical anions in a linear ion trap mass spectrometer. The ion/ion reactions proceed through sodium transfer, electron-transfer, and complex formation. Electron-transfer reactions are shown to give rise to cleavage at each ester linkage with the subsequent loss of a neutral quaternary nitrogen moiety. Electron-transfer without dissociation produces [M + 2Na](+.) radical cations, which undergo collision-induced dissociation (CID) to give products that arise from bond cleavage of each fatty acid chain. The CID of the complex ions yields products similar to those produced directly from the electron-transfer reactions of doubly sodiated GPC, although with different relative abundances. These findings indicate that the analysis of GPC lipids by ETD in conjunction with CID can provide some structural information, such as the number of carbons, degree of unsaturation for each fatty acid substituent, and the positions of the fatty acid substituents; some information about the location of the double bonds may be present in low intensity CID product ions.

Fast Multiple Electron Capture Dissociation in a Linear Radio Frequency Quadrupole Ion Trap

We developed a fast electron capture dissociation (ECD) device using a linear radio frequency-quadrupole (RFQ) ion trap. The device dissociated peptides and proteins using a focused electron beam with an intensity of 0.5 microA and a diameter of 1 mm. The electron capture rate was 13%/ms for doubly charged peptides, and the total amount of ECD products was identical to the theoretical limit, i.e., 50% of incident precursor ions were observed as maximum ECD products by electron irradiation of 7 ms in a pulse counting detection scheme. Coupling this ECD device to a time-of-flight mass spectrometer, we applied multiple ECD. Protonated ubiquitin precursor ions with a charge state of 10 were repeatedly cleaved by ECD, i.e., charge-reduced species and their highly charged fragments were cleaved again and again, creating lower charged products, leaving only singly to triply charged states among the final products. Meanwhile with the amount of electron irradiated, lower charged products increased. Applying an electron beam for 8 ms, we obtained 96% of the total sequence coverage using a 40 fmol sample except at three proline sites. This fast ECD device should be widely applicable to proteomics including post-translational modification analysis and top-down analysis.