Phosphopeptide anion characterization via sequential charge inversion and electron-transfer dissociation

Sequencing of Phosphopeptides Using a Sequential Charge Inversion Ion/Ion Reaction and Electron Capture Dissociation Workflow

Protein phosphorylation, a common post-translational modification (PTM), is fundamental in a plethora of biological processes, most importantly in modulating cell signaling pathways. Matrix-assisted laser desorption/ionization (MALDI) coupled to tandem mass spectrometry (MS/MS) is an attractive method for phosphopeptide characterization due to its high speed, low limit of detection, and surface sampling capabilities. However, MALDI analysis of phosphopeptides is constrained by relatively low abundances in biological samples and poor relative ionization efficiencies in positive ion mode. Additionally, MALDI tends to produce singly charged ions, generally limiting the accessible MS/MS techniques that can be used for peptide sequencing. For example, collision induced dissociation (CID) is readily amendable to the analysis of singly charged ions, but results in facile loss of phosphoric acid, precluding the localization of the PTM. Electron-based dissociation methods (e.g., electron capture dissociation, ECD) are well suited for PTM localization, but require multiply charged peptide cations to avoid neutralization during ECD. Conversely, phosphopeptides are readily ionized using MALDI in negative ion mode. If the precursor ions are first formed in negative ion mode, a gas-phase charge inversion ion/ion reaction could then be used to transform the phosphopeptide anions produced via MALDI into multiply charged cations that are well-suited for ECD. Herein we demonstrate a multistep workflow combining a charge inversion ion/ion reaction that first transforms MALDI-generated phosphopeptide monoanions into multiply charged cations, and then subjects these multiply charged phosphopeptide cations to ECD for sequence determination and phosphate bond localization.

Mass spectrometry of dendrimers

Mass spectrometry (MS) has become an essential technique to characterize dendrimers as it proved efficient at tackling analytical challenges raised by their peculiar onion-like structure. Owing to their chemical diversity, this review covers benefits of MS methods as a function of dendrimer classes, discussing advantages and limitations of ionization techniques, tandem mass spectrometry (MS/MS) strategies to determine the structure of defective species, as well as most recently demonstrated capabilities of ion mobility spectrometry (IMS) in the field. Complementarily, the well-defined structure of these macromolecules offers major advantages in the development of MS-based method, as reported in a second section reviewing uses of dendrimers as MS and IMS calibration standards and as multifunctional charge inversion reagents in gas phase ion/ion reactions.

Electron transfer dissociation mass spectrometry of acidic phosphorylated peptides cationized with trivalent praseodymium

The lanthanide ion praseodymium, Pr(III), was employed to study metallated ion formation and electron transfer dissociation (ETD) of 27 biological and model highly acidic phosphopeptides. All phosphopeptides investigated form metallated ions by electrospray ionization (ESI) that can be studied by ETD to yield abundant sequence information. The ions formed are [M + Pr - H]²⁺ , [M + Pr]³⁺ , and [M + Pr + H]⁴⁺ . All biological phosphopeptides with a chain length of seven or more residues generate [M + Pr]³⁺ . For biological phosphopeptides, [M + Pr]³⁺ undergoes more backbone cleavage by ETD than [M + Pr - H]²⁺ and, in some cases, full sequence coverage occurs. Acidic model phosphorylated hexa-peptides and octa-peptides, composed of alanine residues and one phosphorylated residue, form exclusively [M + Pr - H]²⁺ by ESI. Limited sequence information is obtained by ETD of [M + Pr - H]²⁺ with only metallated product ions being generated. For two biological phosphopeptides, [M + Pr + H]⁴⁺ is observed and may be due to the presence of at least one residue with a highly basic side chain that facilitates the addition of an extra proton. For the model phosphopeptides, more sequence coverage occurs when the phosphorylated residue is in the middle of the sequence than at either the N- or C-terminus. ETD of the metallated precursor ions formed by ESI generates exclusively metallated and nonmetallated c- and z-ions for the biological phosphopeptides, while metallated c-ions, z-ions, and a few y-ions form for the model phosphopeptides. Most of the product ions contain the phosphorylated residue indicating that the metal ion binds predominantly at the deprotonated phosphate group. The results of this study indicate that ETD is a promising tool for sequencing highly acidic phosphorylated peptides by metal adduction with Pr (III) and, by extension, all nonradioactive lanthanide metal ions.

Nanoscale bio-platforms for living cell interrogation: current status and future perspectives

The living cell is a complex entity that dynamically responds to both intracellular and extracellular environments. Extensive efforts have been devoted to the understanding intracellular functions orchestrated with mRNAs and proteins in investigation of the fate of a single-cell, including proliferation, apoptosis, motility, differentiation and mutations. The rapid development of modern cellular analysis techniques (e.g. PCR, western blotting, immunochemistry, etc.) offers new opportunities in quantitative analysis of RNA/protein expression up to a single cell level. The recent entries of nanoscale platforms that include kinds of methodologies with high spatial and temporal resolution have been widely employed to probe the living cells. In this tutorial review paper, we give insight into background introduction and technical innovation of currently reported nanoscale platforms for living cell interrogation. These highlighted technologies are documented in details within four categories, including nano-biosensors for label-free detection of living cells, nanodevices for living cell probing by intracellular marker delivery, high-throughput platforms towards clinical current, and the progress of microscopic imaging platforms for cell/tissue tracking in vitro and in vivo. Perspectives for system improvement were also discussed to solve the limitations remains in current techniques, for the purpose of clinical use in future.

Electron capture dissociation in the analysis of protein phosphorylation

Protein phosphorylation is a widespread and important post-translational modification. Despite recent advances in phosphoproteomic methods, phosphopeptide identification and site localization remain challenging. Electron capture dissociation has inherent advantages for phosphorylation analysis. The use of electron capture dissociation in this area to date is reviewed and future prospects are outlined.

Reagent cluster anions for multiple gas-phase covalent modifications of peptide and protein cations

Multiple gas phase ion/ion covalent modifications of peptide and protein ions are demonstrated using cluster-type reagent anions of N-hydroxysulfosuccinimide acetate (sulfo-NHS acetate) and 2-formyl-benzenesulfonic acid (FBMSA). These reagents are used to selectively modify unprotonated primary amine functionalities of peptides and proteins. Multiple reactive reagent molecules can be present in a single cluster ion, which allows for multiple covalent modifications to be achieved in a single ion/ion encounter and at the 'cost' of only a single analyte charge. Multiple derivatizations are demonstrated when the number of available reactive sites on the analyte cation exceeds the number of reagent molecules in the anionic cluster (e.g., data shown here for reactions between the polypeptide [K10 + 3H](3+) and the reagent cluster [5R(5Na) - Na](-)). This type of gas-phase ion chemistry is also applicable to whole protein ions. Here, ubiquitin was successfully modified using an FBMSA cluster anion which, upon collisional activation, produced fragment ions with various numbers of modifications. Data for the pentamer cluster are included as illustrative of the results obtained for the clusters comprised of two to six reagent molecules.

Gas-phase ion/ion reactions of peptides and proteins: acid/base, redox, and covalent chemistries

Gas-phase ion/ion reactions are emerging as useful and flexible means for the manipulation and characterization of peptide and protein biopolymers. Acid/base-like chemical reactions (i.e., proton transfer reactions) and reduction/oxidation (redox) reactions (i.e., electron transfer reactions) represent relatively mature classes of gas-phase chemical reactions. Even so, especially in regards to redox chemistry, the widespread utility of these two types of chemistries is undergoing rapid growth and development. Additionally, a relatively new class of gas-phase ion/ion transformations is emerging which involves the selective formation of functional-group-specific covalent bonds. This feature details our current work and perspective on the developments and current capabilities of these three areas of ion/ion chemistry with an eye towards possible future directions of the field.

Systematic comparison of ultraviolet photodissociation and electron transfer dissociation for peptide anion characterization

Ultraviolet photodissociation at 193 nm (UVPD) and negative electron transfer dissociation (NETD) were compared to establish their utility for characterizing acidic proteomes with respect to sequence coverage distributions (a measure of product ion signals across the peptide backbone), sequence coverage percentages, backbone cleavage preferences, and fragmentation differences relative to precursor charge state. UVPD yielded significantly more diagnostic information compared with NETD for lower charge states (n ≤ 2), but both methods were comparable for higher charged species. While UVPD often generated a more heterogeneous array of sequence-specific products (b-, y-, c-, z-, Y-, d-, and w-type ions in addition to a- and x- type ions), NETD usually created simpler sets of a/x-type ions. LC-MS/UVPD and LC-MS/NETD analysis of protein digests utilizing high pH mobile phases coupled with automated database searching via modified versions of the MassMatrix algorithm was undertaken. UVPD generally outperformed NETD in stand-alone searches due to its ability to efficiently sequence both lower and higher charge states with rapid activation times. However, when combined with traditional positive mode CID, both methods yielded complementary information with significantly increased sequence coverage percentages and unique peptide identifications over that of just CID alone.

Sequential abundant ion fragmentation analysis (SAIFA): an alternative approach for phosphopeptide identification using an ion trap mass spectrometer

Phosphorylation has been the most studied of all the posttranslational modifications of proteins. Mass spectrometry has emerged as a powerful tool for phosphomapping on proteins/peptides. Collision-induced dissociation (CID) of phosphopeptides leads to the loss of phosphoric or metaphosphoric acid as a neutral molecule, giving an intense neutral loss product ion in the mass spectrum. Dissociation of the neutral loss product ion identifies peptide sequence. This method of data-dependent constant neutral loss (DDNL) scanning analysis has been commonly used for mapping phosphopeptides. However, preferential losses of groups other than phosphate are frequently observed during CID of phosphopeptides. Ions that result from such losses are not identified during DDNL analysis due to predetermined scanning for phosphate loss. In this study, we describe an alternative approach for improved identification of phosphopeptides by sequential abundant ion fragmentation analysis (SAIFA). In this approach, there is no predetermined neutral loss molecule, thereby undergoing sequential fragmentation of abundant peak, irrespective of the moiety lost during CID. In addition to improved phosphomapping, the method increases the sequence coverage of the proteins identified, thereby increasing the confidence of protein identification. To the best of our knowledge, this is the first report to use SAIFA for phosphopeptide identification.

Tandem mass spectrometry strategies for phosphoproteome analysis

Protein phosphorylation is involved in nearly all essential biochemical pathways and the deregulation of phosphorylation events has been associated with the onset of numerous diseases. A multitude of tandem mass spectrometry (MS/MS) and multistage MS/MS (i.e., MS(n) ) strategies have been developed in recent years and have been applied toward comprehensive phosphoproteomic analysis, based on the interrogation of proteolytically derived phosphopeptides. However, the utility of each of these MS/MS and MS(n) approaches for phosphopeptide identification and characterization, including phosphorylation site localization, is critically dependant on the properties of the precursor ion (e.g., polarity and charge state), the specific ion activation method that is employed, and the underlying gas-phase ion chemistries, mechanisms and other factors that influence the gas-phase fragmentation behavior of phosphopeptide ions. This review therefore provides an overview of recent studies aimed at developing an improved understanding of these issues, and highlights the advantages and limitations of both established (e.g., CID) and newly maturing (e.g., ECD, ETD, photodissociation, etc.) yet complementary, ion activation techniques. This understanding is expected to facilitate the continued refinement of existing MS/MS strategies, and the development of novel MS/MS techniques for phosphopeptide analysis, with great promise in providing new insights into the role of protein phosphorylation on normal biological function, and in the onset and progression of disease. © 2011 Wiley Periodicals, Inc., Mass Spec Rev 30:600-625, 2011.

Metastable atom-activated dissociation mass spectrometry of phosphorylated and sulfonated peptides in negative ion mode

The dissociation behavior of phosphorylated and sulfonated peptide anions was explored using metastable atom-activated dissociation mass spectrometry (MAD-MS) and collision-induced dissociation (CID). A beam of high kinetic energy helium (He) metastable atoms was exposed to isolated phosphorylated and sulfonated peptides in the 3- and 2- charge states. Unlike CID, where phosphate losses are dominant, the major dissociation channels observed using MAD were C(α) - C peptide backbone cleavages and neutral losses of CO(2), H(2)O, and [CO(2) + H(2)O] from the charge reduced (oxidized) product ion, consistent with an electron detachment dissociation (EDD) mechanism such as Penning ionization. Regardless of charge state or modification, MAD provides ample backbone cleavages with little modification loss, which allows for unambiguous PTM site determination. The relative abundance of certain fragment ions in MAD is also demonstrated to be somewhat sensitive to the number and location of deprotonation sites, with backbone cleavage somewhat favored adjacent to deprotonated sites like aspartic acid residues. MAD provides a complementary dissociation technique to CID, ECD, ETD, and EDD for peptide sequencing and modification identification. MAD offers the unique ability to analyze highly acidic peptides that contain few to no basic amino acids in either negative or positive ion mode.

Unambiguous characterization of site-specific phosphorylation of leucine-rich repeat Fli-I-interacting protein 2 (LRRFIP2) in Toll-like receptor 4 (TLR4)-mediated signaling

In the TLR4 signaling pathways, we previously characterized a signal regulator, LRRFIP2, that modulates the time course-dependent changes in NF-κB activity through its dynamic interaction with the TLR adaptor protein, MyD88. However, little is known about the driving force behind the LPS-inducible dynamics between LRRFIP2 and MyD88. We have therefore designed a multiplex label-free quantitative proteomics method to investigate dynamic changes of LRRFIP2 phosphorylation upon LPS stimulation. Given our observation that LRRFIP2 binds to MyD88 through its serine-rich domain in which most of serine residues have the propensity to be phosphorylated, we used collision-activated dissociation- and electron transfer dissociation-based methods in a complementary manner to unambiguously localize phosphorylation sites in the peptides constituting the serine-rich domain. Among 23 phosphorylation sites identified and first quantified by the label-free approach and then verified by the AACT/SILAC (amino acid-coded tagging/stable isotope labeling in cell culture)-based quantitation method, phosphorylation at serine 202 showed a significant LPS-induced dynamic change during the full-course cellular response to LPS stimulation. The substitution of serine 202 with nonphosphorylated residues by site-directed mutagenesis resulted in a weakened LRRFIP2-MyD88 interaction and a concurrently reduced activity in downstream NF-κB. Taking these results together, phosphorylation at serine 202 was found to regulate the dynamics of the LRRFIP2-MyD88 interaction, which in turn modulated the strength and duration of TLR4 signaling. Strategically, we have demonstrated the importance of precise identification of the biologically relevant phosphorylation site(s) using comprehensive mass spectrometry-based quantitative proteomics approaches in guiding downstream biological characterization experiments, which could otherwise be both time- and cost-consuming for a large number of phosphorylation possibilities.

Top-down protein characterization facilitated by ion/ion reactions on a quadrupole/time of flight platform

In comparison to bottom-up proteomics approaches, whereby peptides derived from proteolytic digestion are analyzed, top-down approaches, involving direct analysis of intact proteins, provide higher specificity for protein identification and are better-suited for the characterization of sequence variants. However, top-down protein characterization usually requires more sophisticated instrumentation and methodologies to deal with the more complex tandem mass spectra derived from dissociation of high mass multiply charged intact proteins. Gas-phase ion/ion reactions are universally applicable and have proved to be useful in mixture analysis and top-down biomolecule characterization. The coupling of the ion/ion proton transfer reaction in the context of MS/MS has been demonstrated to expand informing power in top-down protein characterization, particularly with platforms that employ electrodynamic ion trap and TOF mass analysis. In addition, probing protein primary structure using ion/ion electron transfer dissociation usually provides extensive structurally informative fragmentation and also allows for the localization of labile PTMs. Here, the performance of the widely used quadrupole/TOF platform, equipped with ion/ion reaction functionality, for top-down protein characterization is summarized, and various methodologies employing ion/ion reactions are reviewed.

Note: A simple dual polarity dual nanoelectrospray ionization source for ion/ion reactions

A continuously operated dual polarity dual nanoelectrospray ionization source has been constructed and tested. A commercial quadrupole ion trap mass spectrometer was modified to accumulate and trap ions of opposite charge. All changes to the commercial three-dimensional quadrupole ion trap have been made external to the instrument outside of the vacuum system. Few hardware modifications were required because the two emitters send ion beams through the same transmission guides. Computer controlled source voltage polarities are switched quickly and efficiently to transmit one of two continuously generated ion beams. With customized software, this design has proved simple to implement and to operate.

Facile identification and quantitation of protein phosphorylation via beta-elimination and Michael addition with natural abundance and stable isotope labeled thiocholine

Herein, we employ the unique chemical properties of the quaternary amine present in thiocholine (2-mercapto-N,N,N-trimethyl-ethanaminium) in conjunction with alkaline beta-elimination and Michael addition (BEMA) reactions for the specific detection, identification, and quantitation of phosphorylated serine/threonine containing peptides. Through replacement of the phosphate with thiocholine, the negative charge on the phosphopeptide is switched to a quaternary amine containing a permanent positive charge. This strategy resulted in a 100-fold increase in ionization sensitivity during ESI (sub-500 amol/microL detection limit) accompanied by a markedly enhanced production of informative peptidic fragment ions during CID that dramatically increase sequence coverage. Moreover, the definitive localization of phosphorylated residues is greatly facilitated through the generation of diagnostic triads of fragmentation ions resulting from peptide bond cleavage and further neutral loss of either trimethylamine (-59 Da) or thiocholine thiolate (-119 Da) during collision induced dissociation (CID) in tandem mass spectrometry (MS(2) and MS(3)). Synthesis of stable isotope labeled thiocholine enabled the quantitation of protein phosphorylation with high precision by ratiometric comparisons using heavy and light thiocholine. Collectively, this study demonstrates a sensitive and efficient strategy for mapping of phosphopeptides by BEMA using thiocholine through the production of a diagnostic repertoire of unique fragment ions during liquid chromatography-tandem mass spectrometry (LC-MS(2)/MS(3)) analyses, facilitating phosphosite identification and quantitative phosphoproteomics.

Mapping N-terminus phosphorylation sites and quantitation by stable isotope dimethyl labeling

We have previously coupled stable isotope dimethyl labeling with IMAC enrichment for quantifying the extent of protein phosphorylation in vivo. The enhanced a(1) signal of dimethylated peptides served as a unique mass tag for unequivocal identification of the N-terminal amino acids. In this study, we demonstrate that the a(1) ion could further assist in mapping the precise phosphorylation site near the N-terminal region and allow the determination of the exact site and level of phosphorylation in one step by stable isotope dimethyl labeling. We show that the a(1) ion signal was suppressed for dimethylated peptides with a phosphorylation site at the N-terminus Ser/Thr residue (N-p*Ser/Thr) but was still enhanced for N-terminus Tyr residue (N-p*Tyr) or internal Ser/Thr residues (-p*Ser/Thr). Based on the dominant de-phosphorylated molecular ions and b-H(3)PO(4) ions for N-p*Ser/Thr, we propose that dimethyl labeling increases the basicity of the N-terminus and accelerates the de-phosphorylation for N-p*Ser/Thr precursors, which, however, suppresses the a(1) ion enhancement due to the resulting unsaturated covalent bond on C(alpha) of the N-terminus amino acid. Using this method, we excluded three Ser/Thr phosphorylation sites in A431 cells, two of which, however, were previously reported to be phosphorylation sites; we confirmed three known phosphorylation sites in A431 cells and quantified their ratios upon EGF treatment. Notably, we identified a novel phosphorylation site on Ser43 residue at N-terminus of the tryptic peptide derived from SVH protein in pregnant rat uteri. SVH protein has not been reported or implied with any phosphorylation event, and our data show that the Ser43 of SVH is an intrinsic phosphorylation site in pregnant rat uteri and that its phosphorylation level was slightly decreased upon c-AMP treatment.

Ion/ion reactions: new chemistry for analytical MS

Gas-phase ion/ion reactions are emerging as flexible means for probing and manipulating analyte ions with particular utility in bioanalysis.

Gas-phase chemistry of multiply charged bioions in analytical mass spectrometry

Ion chemistry has long played an important role in molecular mass spectrometry (MS), as it is central to the use of MS as a structural characterization tool. With the advent of ionization methods capable of producing gaseous ions from large biomolecules, the chemistry of gaseous bioions has become a highly active area of research. Gas-phase biomolecule-ion reactions are usually driven by interactions with neutral molecules, photons, electrons, ions, or surfaces. Ion dissociation or transformation into different ion types can be achieved. The types of reaction products observed depend on the characteristics of the ions, the transformation methods, and the time frame of observation. This review focuses on the gas-phase chemistries of ions derived from the electrospray ionization of peptides, proteins, and oligonucleotides, with particular emphasis on their utility in bioanalysis. Various ion-transformation strategies, which further facilitate structural interrogation by converting ions from one type to another, are also summarized.

Recent advances in capillary and microfluidic platforms with MS detection for the analysis of phosphoproteins

Reversible protein phosphorylation represents a key regulatory mechanism that triggers essential cellular signaling events. The large-scale characterization of protein phosphorylation in a cell represents, therefore, the objective of many biological studies that aim at elucidating the complex signaling pathways that are involved in the progression and/or regression of a disease. The recent implementation of novel MS detection strategies has significantly advanced the capabilities for interrogating the complex cellular phosphoproteome. Simultaneously, the current advent of miniaturized technologies has clearly demonstrated the superior performance of microfluidic instrumentation for bioanalytical and biological applications that cope with speed, sensitivity and throughput-related demands. This review aims at providing an update on the latest developments regarding the interfacing of microfluidic devices with MS detection for exploring the challenging area of phosphoproteomics.

Transmission mode ion/ion reactions in the radiofrequency-only ion guide of hybrid tandem mass spectrometers

Transmission mode ion/ion reactions have been performed within the first quadrupole, the Q0 radiofrequency (RF)-only quadrupole, of two types of hybrid tandem mass spectrometers (viz., triple quadrupole/linear ion trap and QqTOF instruments). These transmission mode reactions involved the storage of either the reagent species and the transmission of the analyte species through the Q0 quadrupole for charge inversion reactions or the storage of the analyte ions and transmission of the reagent ions as in charge reduction experiments. A key advantage to the use of transmission mode ion/ion reactions is that they do not require any instrument hardware modifications to provide interactions of oppositely charged ions and can be implemented in any instrument that contains a quadrupole or linear ion trap. The focus of this work was to investigate the potential of using the RF-only quadrupole ion guide positioned prior to the first mass-resolving element in a tandem mass spectrometer for ion/ion reactions. Two types of exemplary experiments have been demonstrated. One involved a charge inversion reaction and the other involved a charge reduction reaction in conjunction with ion parking. Ion/ion reactions proved to be readily implemented in Q0 thereby adding significantly greater experimental flexibility in the use of ion/ion reaction experiments with hybrid tandem mass spectrometers.

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.

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.

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.

Peptide and protein quantification using iTRAQ with electron transfer dissociation

Electron transfer dissociation (ETD) has become increasingly used in proteomic analyses due to its complementarity to collision-activated dissociation (CAD) and its ability to sequence peptides with post-translation modifications (PTMs). It was previously unknown, however, whether ETD would be compatible with a commonly employed quantification technique, isobaric tags for relative and absolute quantification (iTRAQ), since the fragmentation mechanisms and pathways of ETD differ significantly from CAD. We demonstrate here that ETD of iTRAQ labeled peptides produces c- and z-type fragment ions as well as reporter ions that are unique from those produced by CAD. Exact molecular formulas of product ions were determined by ETD fragmentation of iTRAQ-labeled synthetic peptides followed by high mass accuracy orbitrap mass analysis. These experiments revealed that ETD cleavage of the N-C(alpha) bond of the iTRAQ tag results in fragment ions that could be used for quantification. Synthetic peptide work demonstrates that these fragment ions provide up to three channels of quantification and that the quality is similar to that provided by beam-type CAD. Protein standards were used to evaluate peptide and protein quantification of iTRAQ labeling in conjunction with ETD, beam-type CAD, and pulsed Q dissociation (PQD) on a hybrid ion trap-orbitrap mass spectrometer. For reporter ion intensities above a certain threshold all three strategies provided reliable peptide quantification (average error <10%). Approximately 36%, 8%, and 16% of scans identified fall below this threshold for ETD, HCD, and PQD, respectively. At the protein level, average errors were 2.3%, 1.7%, and 3.6% for ETD, HCD, and PQD, respectively.

Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry

Proteomics has been proposed as one of the key technologies in the postgenomic era. So far, however, the comprehensive analysis of cellular proteomes has been a challenge because of the dynamic nature and complexity of the multitude of proteins in cells and tissues. Various approaches have been established for the analyses of proteins in a cell at a given state, and mass spectrometry (MS) has proven to be an efficient and versatile tool. MS-based proteomics approaches have significantly improved beyond the initial identification of proteins to comprehensive characterization and quantification of proteomes and their posttranslational modifications (PTMs). Despite these advances, there is still ongoing development of new technologies to profile and analyze cellular proteomes more completely and efficiently. In this review, we focus on MS-based techniques, describe basic approaches for MS-based profiling of cellular proteomes and analysis methods to identify proteins in complex mixtures, and discuss the different approaches for quantitative proteome analysis. Finally, we briefly discuss novel developments for the analysis of PTMs. Altered levels of PTM, sometimes in the absence of protein expression changes, are often linked to cellular responses and disease states, and the comprehensive analysis of cellular proteome would not be complete without the identification and quantification of the extent of PTMs of proteins.

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.

Dual electrospray ion source for electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer

A dual electrospray ionization source (ESI) has been modified to simultaneously produce cations and anions, one from each emitter, for performing rapid electron-transfer dissociation (ETD) ion/ion reactions on a hybrid linear ion trap-orbitrap mass spectrometer. Unlike the pulsed dual ESI sources that were used to generate ETD reagent ions, this source separates the emitters in space, rather than time, by physically switching which one is in front of the atmospheric inlet. The new arrangement allows for substantially enhanced spray stability and decreased switching times (<or=30 ms), allowing for more tandem-MS spectra per unit time. Herein, we demonstrate the stability of the ETD anion population and the ability to identify several c- and z-type product ions from multiply protonated peptide cations.

Improved sequencing of oxidized cysteine and methionine containing peptides using electron transfer dissociation

Oxidative modifications to the side chains of sulfur-containing amino acids often limit the number of product ions formed during collision-induced dissociation (CID) and thus make it difficult to obtain sequence information for oxidized peptides. In this work, we demonstrate that electron-transfer dissociation (ETD) can be used to improve the sequence information obtained from peptides with oxidized cysteine and methionine residues. In contrast to CID, ETD is found to be much less sensitive to the side-chain chemistry, enabling extensive sequence information to be obtained in cases where CID fails to provide this information. These results indicate that ETD is a valuable technique for studying oxidatively modified peptides and proteins. In addition, we report a unique and very abundant product ion that is formed in the CID spectra of peptides having N-terminal cysteine sulfinic acid residues. The mechanism for this unique dissociation pathway involves a six-membered cyclic intermediate and leads to the facile loss of NH(3) and SO(2), which corresponds to a mass loss of 81 Da. While the facile nature of this dissociation pathway limits the sequence information present in CID spectra of peptides with N-terminal cysteine sulfinic acid residues, extensive sequence information for these peptides can be obtained with ETD.

Transmission mode ion/ion proton transfer reactions in a linear ion trap

A new method is described for effecting ion/ion proton transfer reactions that involves storage of analyte ions while oppositely charged ions are transmitted through the stored ion population. In this approach, the products are captured and stored in the linear ion trap for subsequent mass analysis. Charge reduction of multiply charged protein ions is used as an example to illustrate the analytical usefulness of this method. In another variation of the transmission mode ion/ion reaction approach, two charge inversion experiments, implemented by passing analyte ions through a population of multiply charged reagent ions in a LIT, are also demonstrated. A pulsed dual ion source approach coupled with a hybrid triple quadrupole/linear ion trap instrument was used to demonstrate these two methods. The results for ion/ion reactions implemented using these so-called "transmission mode" experiments were comparable to those acquired using the more conventional mutual storage mode, both in terms of efficiency and information content of the spectra. An advantage of transmission mode experiments compared with mutual storage mode experiments is that they do not require any specialized measures to be taken to enable the simultaneous storage of oppositely charged ions.

Implementation of electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer

We describe the adaptation of a hybrid quadrupole linear ion trap-orbitrap mass spectrometer to accommodate electron-transfer ion/ion reactions (ETD) for peptide and protein characterization. The method utilizes pulsed, dual electrospray ion sources and requires minimal instrument modification. Switching between cation and reagent anion injection schemes is automated and accomplished within a few hundred milliseconds. Ion/ion reactions are conducted within the linear ion trap, after which the c- and z-type product ions are passed to the orbitrap for high-resolution m/z analysis. With this arrangement, mass accuracies are typically measured to within 2 ppm at a resolving power of approximately 60 000. Using large peptides and intact proteins, we demonstrate such capabilities will accelerate our ability to interrogate high-mass species. To illustrate compatibility with automated data-dependent analysis and subsequent data processing, we couple the technique with an online chromatographic separation of a yeast whole-cell lysate followed by peptide identification using ProSight PC. Fairly long pulsing times and relatively low ET efficiency, as compared to conventional ETD instrumentation, are the main drawbacks of this approach. Still, our results suggest that the implementation of ETD on sensitive, high-resolution, and high-mass accuracy hybrid instrumentation, such as the orbitrap, will substantially propel the emergent fields of middle- and top-down proteomics.

Neutral fragment mass spectra via ambient thermal dissociation of peptide and protein ions

A novel method for the fragmentation of peptide and protein ions at atmospheric pressure outside the mass spectrometer is described. Peptide/protein ions generated by electrosonic spray ionization (ESSI) are carried through a heated coiled metal tube where they fragment. Fragment ions of types a, b, and y are observed for peptides such as angiotensin II and bradykinin. In the case of phosphopeptides, informative b and y ions which preserve the labile phosphate groups are observed in the negative ion mode, which is potentially useful in the location of phosphorylation sites in proteins through chemical analysis of phosphopeptides. The thermal dissociation method extends to proteins such as ubiquitin and myoglobin, giving rise to y-type and other fragment ions. The most important feature of this method is that it also allows characterization of the neutral fragments arising from thermal dissociation by use of on-line corona discharge ionization. This neutral re-ionization experiment is much easier to perform outside the mass spectrometer than as conventionally done, in vacuum. It yields increased structural information from the resulting mass spectra in both the positive and the negative ion modes.

A pulsed triple ionization source for sequential ion/ion reactions in an electrodynamic ion trap

A pulsed triple ionization source, using a common atmosphere/vacuum interface and ion path, has been developed to generate different types of ions for sequential ion/ion reaction experiments in a linear ion trap-based tandem mass spectrometer. The triple ionization source typically consists of a nano-electrospray emitter for analyte formation and two other emitters, an electrospray emitter and an atmospheric pressure chemical ionization emitter or a second nano-electrospray emitter for formation of the two different reagent ions. The three emitters are positioned in a parallel fashion close to the sampling orifice of the tandem mass spectrometer. The potentials applied to each emitter are sequentially pulsed so that desired ions are generated separately in time and space. Sequential ion/ion reactions take place after analyte ions of interest and different set of reagent ions are sequentially injected into a linear ion trap, where axial trapping is effected by applying an auxiliary radio frequency voltage to the end lenses. The pulsed triple ionization source allows independent optimization of each emitter and can be readily coupled to any atmospheric pressure ionization interface with no need for instrument modifications, provided the potentials required to transmit the ion polarity of interest can be synchronized with the emitter potentials. Several sequential ion/ion reactions examples are demonstrated to illustrate the analytical usefulness of the triple ionization source in the study of gas-phase ion/ion chemistry.

Amplification of infrared multiphoton dissociation efficiency in a quadruple ion trap using IR-active ligands

A strategy for increasing the efficiency of infrared multiphoton dissociation (IRMPD) in a quadrupole ion trap (QIT) is described. IR-active ligands (IRALs) are incorporated into noncovalent complexes of the type [M2+(analyte) IRAL]+, where M is a transition metal such as copper or cobalt and IRAL is an auxiliary ligand with an IR-active phosphonate functional group. The complexes are formed via self-assembly in solution directly prior to ESI-MS analysis. We demonstrate this new IRMPD approach for the structural characterization of flavonoids. The fragment ions obtained by IRMPD are similar to those obtained by CAD and allow facile isomer differentiation of flavonoids. Fourier transform infrared absorption attenuated total reflectance (FTIR-ATR) and energy-variable CAD experiments indicate that the high IRMPD efficiencies stem from the very large IR absorptivities of the IR-active ligands.

Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors

Electron-transfer dissociation (ETD) delivers the unique attributes of electron capture dissociation to mass spectrometers that utilize radio frequency trapping-type devices (e.g., quadrupole ion traps). The method has generated significant interest because of its compatibility with chromatography and its ability to: (1) preserve traditionally labile post-translational modifications (PTMs) and (2) randomly cleave the backbone bonds of highly charged peptide and protein precursor ions. ETD, however, has shown limited applicability to doubly protonated peptide precursors, [M + 2H]2+, the charge and type of peptide most frequently encountered in "bottom-up" proteomics. Here we describe a supplemental collisional activation (CAD) method that targets the nondissociated (intact) electron-transfer (ET) product species ([M + 2H]+*) to improve ETD efficiency for doubly protonated peptides (ETcaD). A systematic study of supplementary activation conditions revealed that low-energy CAD of the ET product population leads to the near-exclusive generation of c- and z-type fragment ions with relatively high efficiency (77 +/- 8%). Compared to those formed directly via ETD, the fragment ions were found to comprise increased relative amounts of the odd-electron c-type ions (c+*) and the even-electron z-type ions (z+). A large-scale analysis of 755 doubly charged tryptic peptides was conducted to compare the method (ETcaD) to ion trap CAD and ETD. ETcaD produced a median sequence coverage of 89%-a significant improvement over ETD (63%) and ion trap CAD (77%).

Strategy for the Identification of Sites of Phosphorylation in Proteins: Neutral Loss Triggered Electron Capture Dissociation

We have previously demonstrated the suitability of data-dependent electron capture dissociation (ECD) for incorporation into proteomic strategies. The ability to directly determine sites of phosphorylation is a major advantage of electron capture dissociation; however, the low stoichiometry associated with phosphorylation means that phosphopeptides are often overlooked in data-dependent ECD analyses. In contrast, collision-induced dissociation (CID) tends to result in loss of the labile phosphate group, often at the expense of sequence fragments. Here, we demonstrate a novel strategy for the characterization of phosphoproteins which exploits the neutral loss feature of CID such that focused ECD of phosphopeptides is achieved. Peptides eluting from a liquid chromatograph are first subjected to CID, and if a neutral loss of 98 Da (corresponding to H3PO4) from the precursor is observed, ECD of that same precursor is performed; i.e., the method comprises neutral loss triggered ECD (NL-ECD-MS/MS). The method was applied to tryptic digests of beta-casein and alpha-casein. For alpha-casein, four sites of phosphorylation were identified with NL-ECD-MS/MS compared with a single site identified by ECD-MS/MS. The method also resulted in ECD of a doubly phosphorylated peptide. A further benefit of the method is that overall protein sequence coverage is improved. Sequence information from nonphosphorylated peptides is obtained as a result of the CID step.

Implementation of ion/ion reactions in a quadrupole/time-of-flight tandem mass spectrometer

A commercial quadrupole/time-of-flight (QqTOF) tandem mass spectrometer has been adapted for ion/ion reaction studies. To enable mutual storage of oppositely charged ions in a linear ion trap, the oscillating quadrupole field of the second quadrupole of the system (Q2) serves to store ions in the radial dimension while auxiliary radio frequency is superposed on the end lenses of Q2 during the reaction period to create barriers in the axial dimension. A pulsed dual electrospray (ESI) source is directly coupled to the instrument interface for the purpose of proton transfer reactions. Singly and doubly charged protein ions as high in mass as 66 kDa are readily formed and observed after proton-transfer reactions. For the modified instrument, the mass resolving power is approximately 8000 for a wide m/z range, and the mass accuracy is approximately 20 ppm for external calibration and approximately 5 ppm for internal calibration after ion/ion reactions. Parallel ion parking is demonstrated with a six-component protein mixture, which shows the potential application of reducing spectral complexity and concentrating certain charge states. The current system has high flexibility with respect to defining MS(n) experiments involving collision-induced dissociation (CID) and ion/ion reactions. Protein precursor and CID product masses can be determined with good accuracy, providing an attractive platform for top-down proteomics. Electron transfer dissociation ion/ion reactions are implemented by using a pulsed nano-ESI/atmospheric pressure chemical ionization dual source for ionization. The reaction between protonated peptide ions and radical anions of 1,3-dinitrobenzene formed exclusively c- and z-type fragment ions.