Selective, sensitive, and rapid phosphopeptide identification in enzymatic digests using ESI-FTICR-MS with infrared multiphoton dissociation

Enhancing Top-Down Analysis Using Chromophore-Assisted Infrared Multiphoton Dissociation from (Phospho)peptides to Protein Assemblies

Infrared multiphoton dissociation (IRMPD) has been used in mass spectrometry to fragment peptides and proteins, providing fragments mostly similar to collisional activation. Using the 10.6 μm wavelength of a CO2 laser, IRMPD suffers from the relative low absorption cross-section of peptides and small proteins. Focusing on top-down analysis, we investigate different means to tackle this issue. We first reassess efficient sorting of phosphopeptides from nonphosphopeptides based on IR-absorption cross-sectional enhancement by phosphate moieties. We subsequently demonstrate that a myo-inositol hexakisphosphate (IP6) noncovalent adduct can substantially enhance IRMPD for nonphosphopeptides and that this strategy can be extended to proteins. As a natural next step, we show that native phospho-proteoforms of proteins display a distinct and enhanced fragmentation, compared to their unmodified counterparts, facilitating phospho-group site localization. We then evaluate the impact of size on the IRMPD of proteins and their complexes. When applied to protein complexes ranging from a 365 kDa CRISPR-Cas Csy ribonucleoprotein hetero-decamer, a 800 kDa GroEL homo-tetradecamer in its apo-form or loaded with its ATP cofactor, to a 1 MDa capsid-like homo-hexacontamer, we conclude that while phosphate moieties present in crRNA and ATP molecules enhance IRMPD, an increase in the IR cross-section with the size of the protein assembly also favorably accrues dissociation yields. Overall, our work showcases the versatility of IRMPD in the top-down analysis of peptides, phosphopeptides, proteins, phosphoproteins, ribonucleoprotein assemblies, and large protein complexes.

Facile Determination of Phosphorylation Sites in Peptides Using Two-Dimensional Mass Spectrometry

Detection and characterization of phosphopeptides by infrared multiphoton dissociation two-dimensional mass spectrometry (IRMPD 2DMS) is shown to be particularly effective. A mixture of phosphopeptides was analyzed by 2DMS without any prior separation. 2DMS enables the data independent analysis of the mixture and the correlation of the fragments to their precursor ions. The extraction of neutral loss lines corresponding to the loss of phosphate under IRMPD fragmentation allows the selective identification of phosphopeptides. Resonance of the 10.6 μm infrared radiation with the vibrational modes of the phosphate functional group produced efficient absorption and high cleavage coverage of the phosphopeptides at much lower irradiation fluence than for nonphosphorylated peptides improving discrimination. Additionally, the localization of the phosphate group was determined.

Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications

Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment. IRMPD spectroscopy is clearly not a proteomics tool. It is rather a valuable source of information for fixed wavelength IRMPD exploited in dissociation protocols of peptides and proteins. Indeed, from the large variety of model PTM containing amino acids and peptides which have been characterized by IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be derived. High throughput workflows relying on the selective fragmentation of modified peptides within a complex mixture have thus been proposed. Sequential fragmentations can be observed upon IR activation, which do not only give rise to rich fragmentation patterns but also overcome low mass cutoff limitations in ion trap mass analyzers. Laser-based vibrational spectroscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the variety of chemical issues coped with and in the technological advancements and implementations.

Ion/ion Charge Inversion/Attachment in Conjunction with Dipolar DC Collisional Activation as a Selective Screen for Sulfo- and Phosphopeptides

We describe a gas-phase approach for the rapid screening of polypeptide anions for phosphorylation or sulfonation based on binding strengths to guanidinium-containing reagent ions. The approach relies on the generation of a complex via reaction of mixtures of deprotonated polypeptide anions with dicationic guanidinium-containing reagent ions and subsequent dipolar DC collisional activation of the complexes. The relative strengths of the electrostatic interactions of guanidinium with deprotonated acidic sites follows the order carboxylate<phosph(on)ate<sulf(on)ate. The differences between the binding strengths at these sites allows for the use of an appropriately selected dipolar DC amplitude to lead to significantly different dissociation rates for complexes derived from unmodified peptides versus phosphorylated and sulfated peptides. The difference in binding strengths between guanidinium and phosph(on)ate versus guanidinium and sulf(on)ate is sufficiently great to allow for the dissociation of a large fraction of phosphopeptide complexes with the dissociation of a much smaller fraction of sulfopeptide complexes. DFT calculations and experimental data with model peptides and with a mixture of tryptic peptides spiked with phosphopeptides are presented to illustrate and support this approach. Dissociation rate data are presented that demonstrate the differences in binding strengths for different anion charge-bearing sites and that reveal the DDC conditions most likely to provide the greatest discrimination between unmodified peptides, phosphopeptides, and sulfopeptides.

Targeted Annotation of S-Sulfonylated Peptides by Selective Infrared Multiphoton Dissociation Mass Spectrometry

Protein S-sulfinylation (R-SO₂^-) and S-sulfonylation (R-SO₃^-) are irreversible oxidative post-translational modifications of cysteine residues. Greater than 5% of cysteines are reported to occupy these higher oxidation states, which effectively inactivate the corresponding thiols and alter the electronic and physical properties of modified proteins. Such higher oxidation states are reached after excessive exposure to cellular oxidants, and accumulate across different disease states. Despite widespread and functionally relevant cysteine oxidation across the proteome, there are currently no robust methods to profile higher order cysteine oxidation. Traditional data-dependent liquid chromatography/tandem mass spectrometry (LC/MS/MS) methods generally miss low-occupancy modifications in complex analyses. Here, we present a data-independent acquisition (DIA) LC/MS-based approach, leveraging the high IR absorbance of sulfoxides at 10.6 μm, for selective dissociation and discovery of S-sulfonated peptides. Across peptide standards and protein digests, we demonstrate selective infrared multiphoton dissociation (IRMPD) of S-sulfonated peptides in the background of unmodified peptides. This selective DIA IRMPD LC/MS-based approach allows identification and annotation of S-sulfonated peptides across complex mixtures while providing sufficient sequence information to localize the modification site.

Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation

Negative mode proteome analysis offers access to unique portions of the proteome and several acidic post-translational modifications; however, traditional collision-based fragmentation methods fail to reliably provide sequence information for peptide anions. Negative electron transfer dissociation (NETD), on the other hand, can sequence precursor anions in a high-throughput manner. Similar to other ion-ion methods, NETD is most efficient with peptides of higher charge state because of the increased electrostatic interaction between reacting molecules. Here we demonstrate that NETD performance for lower charge state precursors can be improved by altering the reagent cation. Specifically, the recombination energy of the NETD reaction-largely dictated by the ionization energy (IE) of the reagent cation-can affect the extent of fragmentation. We compare the NETD reagent cations of C₁₆H₁₀^●+ (IE = 7.9 eV) and SF₅^●+ (IE = 9.6 eV) on a set of standard peptides, concluding that SF₅^●+ yields greater sequence ion generation. Subsequent proteome-scale nLC-MS/MS experiments comparing C₁₆H₁₀^●+ and SF₅^●+ further supported this outcome: analyses using SF₅^●+ yielded 4637 peptide spectral matches (PSMs) and 2900 unique peptides, whereas C₁₆H₁₀^●+ produced 3563 PSMs and 2231 peptides. The substantive gain in identification power with SF₅^●+ was largely driven by improved identification of doubly deprotonated precursors, indicating that increased NETD recombination energy can increase product ion yield for low charge density precursors. This work demonstrates that SF₅^●+ is a viable, if not favorable, reagent cation for NETD, and provides improved fragmentation over the commonly used fluoranthene reagent. Graphical Abstract ᅟ.

Phosphoproteomics with Activated Ion Electron Transfer Dissociation

The ability to localize phosphosites to specific amino acid residues is crucial to translating phosphoproteomic data into biological meaningful contexts. In a companion manuscript ( Anal. Chem. 2017 , DOI: 10.1021/acs.analchem.7b00213 ), we described a new implementation of activated ion electron transfer dissociation (AI-ETD) on a quadrupole-Orbitrap-linear ion trap hybrid MS system (Orbitrap Fusion Lumos), which greatly improved peptide fragmentation and identification over ETD and other supplemental activation methods. Here we present the performance of AI-ETD for identifying and localizing sites of phosphorylation in both phosphopeptides and intact phosphoproteins. Using 90 min analyses we show that AI-ETD can identify 24,503 localized phosphopeptide spectral matches enriched from mouse brain lysates, which more than triples identifications from standard ETD experiments and outperforms ETcaD and EThcD as well. AI-ETD achieves these gains through improved quality of fragmentation and MS/MS success rates for all precursor charge states, especially for doubly protonated species. We also evaluate the degree to which phosphate neutral loss occurs from phosphopeptide product ions due to the infrared photoactivation of AI-ETD and show that modifying phosphoRS (a phosphosite localization algorithm) to include phosphate neutral losses can significantly improve localization in AI-ETD spectra. Finally, we demonstrate the utility of AI-ETD in localizing phosphosites in α-casein, an ∼23.5 kDa phosphoprotein that showed eight of nine known phosphorylation sites occupied upon intact mass analysis. AI-ETD provided the greatest sequence coverage for all five charge states investigated and was the only fragmentation method to localize all eight phosphosites for each precursor. Overall, this work highlights the analytical value AI-ETD can bring to both bottom-up and top-down phosphoproteomics.

193 nm Ultraviolet Photodissociation Mass Spectrometry for Phosphopeptide Characterization in the Positive and Negative Ion Modes

Advances in liquid chromatography tandem mass spectrometry (LC-MS/MS) have permitted phosphoproteomic analysis on a grand scale, but ongoing challenges specifically associated with confident phosphate localization continue to motivate the development of new fragmentation techniques. In the present study, ultraviolet photodissociation (UVPD) at 193 nm is evaluated for the characterization of phosphopeptides in both positive and negative ion modes. Compared to the more standard higher energy collisional dissociation (HCD), UVPD provided more extensive fragmentation with improved phosphate retention on product ions. Negative mode UVPD showed particular merit for detecting and sequencing highly acidic phosphopeptides from alpha and beta casein, but was not as robust for larger scale analysis because of lower ionization efficiencies in the negative mode. HeLa and HCC70 cell lysates were analyzed by both UVPD and HCD. While HCD identified more phosphopeptides and proteins compared to UVPD, the unique matches from UVPD analysis could be combined with the HCD data set to improve the overall depth of coverage compared to either method alone.

Full-Featured Search Algorithm for Negative Electron-Transfer Dissociation

Negative electron-transfer dissociation (NETD) has emerged as a premier tool for peptide anion analysis, offering access to acidic post-translational modifications and regions of the proteome that are intractable with traditional positive-mode approaches. Whole-proteome scale characterization is now possible with NETD, but proper informatic tools are needed to capitalize on advances in instrumentation. Currently only one database search algorithm (OMSSA) can process NETD data. Here we implement NETD search capabilities into the Byonic platform to improve the sensitivity of negative-mode data analyses, and we benchmark these improvements using 90 min LC-MS/MS analyses of tryptic peptides from human embryonic stem cells. With this new algorithm for searching NETD data, we improved the number of successfully identified spectra by as much as 80% and identified 8665 unique peptides, 24 639 peptide spectral matches, and 1338 proteins in activated-ion NETD analyses, more than doubling identifications from previous negative-mode characterizations of the human proteome. Furthermore, we reanalyzed our recently published large-scale, multienzyme negative-mode yeast proteome data, improving peptide and peptide spectral match identifications and considerably increasing protein sequence coverage. In all, we show that new informatics tools, in combination with recent advances in data acquisition, can significantly improve proteome characterization in negative-mode approaches.

The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD)

The field of proteomics almost uniformly relies on peptide cation analysis, leading to an underrepresentation of acidic portions of proteomes, including relevant acidic posttranslational modifications. Despite the many benefits negative mode proteomics can offer, peptide anion analysis remains in its infancy due mainly to challenges with high-pH reversed-phase separations and a lack of robust fragmentation methods suitable for peptide anion characterization. Here, we report the first implementation of activated ion negative electron transfer dissociation (AI-NETD) on the chromatographic timescale, generating 7,601 unique peptide identifications from Saccharomyces cerevisiae in single-shot nLC-MS/MS analyses of tryptic peptides-a greater than 5-fold increase over previous results with NETD alone. These improvements translate to identification of 1,106 proteins, making this work the first negative mode study to identify more than 1,000 proteins in any system. We then compare the performance of AI-NETD for analysis of peptides generated by five proteases (trypsin, LysC, GluC, chymotrypsin, and AspN) for negative mode analyses, identifying as many as 5,356 peptides (1,045 proteins) with LysC and 4,213 peptides (857 proteins) with GluC in yeast-characterizing 1,359 proteins in total. Finally, we present the first deep-sequencing approach for negative mode proteomics, leveraging offline low-pH reversed-phase fractionation prior to online high-pH separations and peptide fragmentation with AI-NETD. With this platform, we identified 3,467 proteins in yeast with trypsin alone and characterized a total of 3,730 proteins using multiple proteases, or nearly 83% of the expressed yeast proteome. This work represents the most extensive negative mode proteomics study to date, establishing AI-NETD as a robust tool for large-scale peptide anion characterization and making the negative mode approach a more viable platform for future proteomic studies.

Identification of two arginine kinase forms of endoparasitoid Leptomastix dactylopii venom by bottom up-sequence tag approach

Leptomastix dactylopii (Howard) is an endoparasitoid wasp, natural enemy of mealybug Planococcus citri (Risso). Despite the acquired knowledge regarding this host-parasitoid interaction, only little information is available on the factors of parasitoid origin able to modulate the mealybug physiology. The major alteration observed in P. citri is a strong reduction in fecundity, which is evident soon after parasitization by L. dactylopii or venom injection in unparasitized hosts indicating that this proteinaceus secretion injected at the oviposition plays a key-role in host regulation. Protein identification of L. dactilopii venom has been limited by the lack of literature sources and public protein databases. Here, we identified two venom proteins by an integrated trascriptomic and proteomic approach. A custom-made transcriptomic database from the L. dactylopii venom glands was created by applying the high-throughput RNA sequencing approach. Two-dimensional gel electrophoresis (2DE) trypsinized protein spots were analyzed by high-resolution mass spectrometry (FTICRMS-12 T). The most abundant peptide ions were fragmented by collision induced dissociation and the obtained sequence tags were subjected to custom-made protein database searching. Two putative arginine kinases (full-length and truncated form) were identified. This is the first case in which both, truncated and full length arginine kinases, are identified in an endoparasitoid non-paralyzing venom.

Differentiating sulfopeptide and phosphopeptide ions via resonant infrared photodissociation

The post-translational modifications sulfation and phosphorylation pose special challenges to mass spectral analysis due to their isobaric nature and their lability in the gas phase, as both types of peptides dissociate through similar channels upon collisional activation. Here, we present resonant infrared photodissociation based on diagnostic sulfate and phosphate OH stretches, as a means to differentiate sulfated from phosphorylated peptides within the framework of a mass spectrometry platform. The approach is demonstrated for a number of tyrosine-containing peptides, ranging from dipeptides (YG, pYG, and sYG) over tripeptides (GYR, GpYR, and GsYR), to more biologically relevant enkephalin peptides (YGGFL, pYGGFL, and sYGGFL). In all cases, the diagnostic ranges for sulfate OH stretches are established as 3580-3600 cm(-1) and can thus be distinguished from other characteristic hydrogen stretches, such as carboxylic acid OH, alcohol OH, and phosphate OH stretches.

Femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fsLID-MS/MS) of deprotonated phosphopeptide anions

RATIONALE

Radical-directed dissociation techniques provide structural information which is complementary to that from conventional collision-induced dissociation (CID). The analysis of phosphopeptide anions is warranted due to their relatively acidic character. As femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fsLID-MS/MS) is uniquely initiated by field ionization, an investigation is warranted to determine whether fsLID may provide novel analytical utility for phosphopeptide anions.

METHODS

Twenty-three synthetic deprotonated phosphopeptide anions were introduced into a three-dimensional quadrupole ion trap mass spectrometer via electrospray ionization. The ion trap was interfaced with a near-IR (802 nm) ultrashort-pulsed (35 fs FWHM) ultrahigh-powered (peak power ~10(14)  W/cm(2)) laser system. Performance comparisons are made with other techniques applied to phosphopeptide anion analysis, including CID, electron detachment dissociation (EDD), negative electron transfer dissociation (NETD), activated electron photodetachment dissociation (activated-EPD), and ultraviolet photodissociation (UVPD).

RESULTS

FsLID-MS/MS of multiply deprotonated phosphopeptide anions provides sequence information via phosphorylation-intact a/x ions in addition to other sequence ions, satellite ions, and side-chain losses. Novel fragmentation processes include selective c-ion formation N-terminal to Ser/Thr and a phosphorylation-specific correlation between xn -98 ion abundances and phosphorylation at the n(th) residue. Sequencing-quality data required about 30 s of signal averaging. fsLID-MS/MS of singly deprotonated phosphopeptides did not yield product anions with stable trajectories, despite significant depletion of the precursor.

CONCLUSIONS

Multiply deprotonated phosphopeptide anions were sequenced via negative-mode fsLID-MS/MS, with phosphosite localization facilitated by a/x ion series in addition to diagnostic x(n)-98 ions. fsLID-MS/MS is qualitatively competitive with other techniques. Further efficiency enhancements (e.g., implementation on a linear trap or/and higher pulse frequencies) may permit sequence analyses on chromatographic timescales.

Activated ion ETD performed in a modified collision cell on a hybrid QLT-Oribtrap mass spectrometer

We describe the implementation and characterization of activated ion electron transfer dissociation (AI-ETD) on a hybrid QLT-Orbitrap mass spectrometer. AI-ETD was performed using a collision cell that was modified to enable ETD reactions, in addition to normal collisional activation. The instrument manifold was modified to enable irradiation of ions along the axis of this modified cell with IR photons from a CO2 laser. Laser power settings were optimized for both charge (z) and mass to charge (m/z) and the instrument control firmware was updated to allow for automated adjustments to the level of irradiation. This implementation of AI-ETD yielded 1.6-fold more unique identifications than ETD in an nLC-MS/MS analysis of tryptic yeast peptides. Furthermore, we investigated the application of AI-ETD on large scale analysis of phosphopeptides, where laser power aids ETD, but can produce b- and y-type ions because of the phosphoryl moiety's high IR adsorption. nLC-MS/MS analysis of phosphopeptides derived from human embryonic stem cells using AI-ETD yielded 2.4-fold more unique identifications than ETD alone, demonstrating a promising advance in ETD sequencing of PTM containing peptides.

Structures of biomolecular ions in the gas phase probed by infrared light sources

Infrared (IR) spectroscopy of biomolecular ions combines mass spectrometry's high sensitivity and ability to analyze complex mixtures with the enhanced structural information available from vibrational spectroscopy. IR spectroscopy is in principle well placed to distinguish isomers and allow chemical classification of unknown molecules. This review gives an outline of current instrumentation, spectroscopic approaches, and potential bottlenecks. We discuss the most promising applications in bioanalytical mass spectrometry in view of recent experimental results, as well as future applications based on bioinformatics.

Electron detachment dissociation and negative ion infrared multiphoton dissociation of electrosprayed intact proteins

In top-down proteomics, intact gaseous proteins are fragmented in a mass spectrometer by, e.g., electron capture dissociation (ECD) to obtain structural information. By far, most top-down approaches involve dissociation of protein cations. However, in electrospray ionization of phosphoproteins, the high acidity of phosphate may contribute to the formation of intramolecular hydrogen bonds or salt bridges, which influence subsequent fragmentation behavior. Other acidic proteins or proteins with regions containing multiple acidic residues may also be affected similarly. Negative ion mode, on the other hand, may enhance deprotonation and unfolding of multiply phosphorylated or highly acidic protein regions. Here, activated ion electron detachment dissociation (AI-EDD) and negative ion infrared multiphoton dissociation (IRMPD) were employed to investigate the fragmentation of intact proteins, including multiply phosphorylated β-casein, calmodulin, and glycosylated ribonuclease B. Compared to AI-ECD and positive ion IRMPD, AI-EDD and negative ion IRMPD provide complementary protein sequence information, particularly in regions with high acidity, including the multiply phosphorylated region of β-casein.

IR and UV photodissociation as analytical tools for characterizing lipid A structures

The utility of 193-nm ultraviolet photodissociation (UVPD) and 10.6-μm infrared multiphoton dissociation (IRMPD) for the characterization of lipid A structures was assessed in an ion trap mass spectrometer. The fragmentation behavior of lipid A species was also evaluated by activated-electron photodetachment (a-EPD), which uses 193-nm photons to create charge reduced radicals that are subsequently dissociated by collisional activation. In contrast to collision-induced dissociation (CID), IRMPD offered the ability to selectively differentiate product ions with varying degrees of phosphorylation because of the increased photoabsorption cross sections and thus dissociation of phosphate-containing species. Both 193-nm UVPD and a-EPD yielded higher abundances and a larger array of product ions arising from C-C cleavages, as well as cross-ring and inter-ring glucosamine cleavages, compared to CID and IRMPD, because of high energy, single-photon absorption, and/or radical-directed dissociation. UVPD at 193 nm also exhibited enhanced cleavage between the amine and carbonyl groups on the 2- and 2'-linked primary acyl chains. Lastly, UVPD of phosphorylethanolamine-modified lipid A species resulted in preferential cleavage of the C-O bond between ethanolamine and phosphate, enabling the selective identification of this modification.

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.

Implementing photodissociation in an Orbitrap mass spectrometer

We modified a dual pressure linear ion trap Orbitrap to permit infrared multiphoton dissociation (IRMPD) in the higher energy collisional dissociation (HCD) cell for high resolution analysis. A number of parameters, including the pressures of the C-trap and HCD cell, the radio frequency (rf) amplitude applied to the C-trap, and the HCD DC offset, were evaluated to optimize IRMPD efficiency and maintain a high signal-to-noise ratio. IRMPD was utilized for characterization of phosphopeptides, supercharged peptides, and N-terminal modified peptides, as well as for top-down protein analysis. The high resolution and high mass accuracy capabilities of the Orbitrap analyzer facilitated confident assignment of product ions arising from IRMPD.

193-nm photodissociation of singly and multiply charged peptide anions for acidic proteome characterization

193-nm ultraviolet photodissociation (UVPD) was implemented to sequence singly and multiply charged peptide anions. Upon dissociation by this method, a-/x-type, followed by d and w side-chain loss ions, were the most prolific and abundant sequence ions, often yielding 100% sequence coverage. The dissociation behavior of singly and multiply charged anions was significantly different with higher charged precursors yielding more sequence ions; however, all charge states investigated (1- through 3-) produced rich diagnostic information. UVPD at 193  nm was also shown to successfully differentiate and pinpoint labile phosphorylation modifications. The sequence ions were produced with high abundances, requiring limited averaging for satisfactory spectral quality. The intact, charge-reduced radical products generated by UV photoexcitation were also subjected to collision-induced dissociation (termed, activated-electron photodetachment dissociation (a-EPD)), but UVPD alone yielded more predictable and higher abundance sequence ions. With the use of a basic (pH∼11.5), piperidine-modified mobile phase, LC-MS/UVPD was implemented and resulted in the successful analysis of mitogen-activated pathway kinases (MAPKs) using ultrafast activation times (5  ns).

Activated-ion electron transfer dissociation improves the ability of electron transfer dissociation to identify peptides in a complex mixture

Using a modified electron transfer dissociation (ETD)-enabled quadrupole linear ion trap (QLT) mass spectrometer, we demonstrate the utility of IR activation concomitant with ETD ion-ion reactions (activated-ion ETD, AI-ETD). Analyzing 12 strong cation exchanged (SCX) fractions of a LysC digest of human cell protein extract using ETD, collision-activated dissociation (CAD), and AI-ETD, we find that AI-ETD generates 13 405 peptide spectral matches (PSMs) at a 1% false-discovery rate (1% FDR), surpassing both ETD (7 968) and CAD (10 904). We also analyze 12 SCX fractions of a tryptic digest of human cell protein extract and find that ETD produces 6 234 PSMs, AI-ETD 9 130 PSMs, and CAD 15 209 PSMs. Compared to ETD with supplemental collisional activation (ETcaD), AI-ETD generates ∼80% more PSMs for the whole cell lysate digested with trypsin and ∼50% more PSMs for the whole cell lysate digested with LysC.

Natural structural motifs that suppress peptide ion fragmentation after electron capture

Series of doubly and triply protonated diarginated peptide molecules with different number of glutamic acid (E) and asparagine (N) residues were analyzed under ECD conditions. ECD spectra of doubly-protonated peptides show a strong dependence on the number of E and N residues. Both the backbone cleavages and hydrogen radical (H*) loss from the charge-reduced precursor ions ([M+2H](+*)) were suppressed as the number of E and N residues increases. A strong inhibition of the backbone cleavages and H* loss from [M+2H](+*) was found for peptides with 6E residues (or 4E + 2N residues). The results obtained using these model peptides were re-confirmed by analyzing N-arginated Fibrinopeptide-B (i.e., REGVNDNEEGFFSAR). In contrast to the N-arginated peptide, ECD of the doubly-protonated Fibrinopeptide-B and its analogues show extensive backbone cleavages leading to series of c- and z-ions ( approximately 80% sequence coverage). Based on these results, it is believed that peptide ions with all surplus protons sequestered in arginine-residues would show enhanced stability under ECD conditions as the number of acid-residue increases. The suppression of backbone cleavages and H* loss from [M+2H](+*) are presumably attributed to the low reactivity of the charge-reduced precursor ions. One of the possible hypothesis is that diarginated E-rich peptides may contain hydrogen bonds between carbonyl oxygen of E side chains and backbone amide hydrogen. These hydrogen bonds would provide extra stabilization for [M+2H](+*). This is the first demonstration of natural structural motifs in peptides that would inhibit the backbone fragmentation of the charge-reduced peptide ions under ECD conditions.

Top-down protein fragmentation by infrared multiphoton dissociation in a dual pressure linear ion trap

Infrared multiphoton dissociation (IRMPD) was implemented in a novel dual pressure linear ion trap for rapid top-down proteomics. The high pressure cell provided improved trapping and isolation efficiencies while the isotopic profiles of 10+ charged ions could be resolved by mass analysis in the low pressure cell that enabled effective top down protein identification. Striking differences between IRMPD in the low pressure cell and CID in the high pressure cell were observed for proteins ranging from 8.6 to 29 kDa. Because of secondary dissociation, IRMPD yielded product ions in significantly lower charge states as compared to CID, thus facilitating more accurate mass identification and streamlining product ion assignment. This outcome was especially useful for database searching of larger proteins (approximately 29 kDa) as IRMPD substantially improved protein identification and scoring confidence. Also, IRMPD showed an increased selectivity toward backbone cleavages N-terminal to proline and C-terminal to acidic residues (especially for the lowest charge states), which could be useful for a priori spectral predictions and enhanced database searching for protein identification.

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.

Ultraviolet photodissociation mass spectrometry of bis-aryl hydrazone conjugated peptides

Ultraviolet photodissociation (UVPD) at 355 nm was used to rapidly identify peptides which had been chemically conjugated through bis-aryl hydrazone (BAH) moieties. The two biomolecules of interest were separately tagged to introduce either an aldehyde or a hydrazine and then conjugated together through these functional groups to from the UV-chromogenic BAH-group. In a mock mixture of peptides, UVPD was used to screen for the BAH-conjugated peptides in direct infusion ESI-UVPD-MS and online LC-UVPD-MS methods by comparing the abundances of the ions with the laser off and with the laser on. Only the BAH-conjugated peptides were observed to photodissociate upon exposure to UV irradiation, thus affording excellent selectivity for the pinpointing the relevant conjugated peptides in a complex mixture of nonconjugated peptides. UVPD analysis of conjugated model peptides indicated that the UVPD efficiencies of these species were charge state dependent. BAH-conjugated peptides that had a mobile proton which could protonate the basic BAH-moiety underwent more efficient photodissociation than the peptide ions with sequestered protons. Ultraviolet photodissociation of BAH-cross-linked peptides also yielded more diagnostic sequence ions than CID to unambiguously locate the site of conjugation.

Gas-phase intramolecular phosphate shift in phosphotyrosine-containing peptide monoanions

Phosphotyrosine-containing peptide monoanions [M-H](-) exhibit extensive neutral loss of phosphoric acid (98 Da) upon quadrupole time-of-flight and ion-trap collision-induced dissociation (CID). In contrast, a neutral loss of metaphosphoric acid HPO(3) (80 Da) is negligible from the deprotonated phosphotyrosine peptides. The efficient H(3)PO(4) release is unexpected, given the structure of phosphotyrosine. Our study reveals that the abundant [M-H-98](-) product ions of pTyr-peptides are not a result of consecutive losses of HPO(3) and H(2)O but, rather, are induced by an intramolecular interaction of the phosphotyrosine phosphate with deprotonated peptide functions such as hydroxyl, carboxyl, and to a small extent, amide. As a result, an internal phosphotyrosine phosphate shift occurs, and the obtained phosphorylated functionalities undergo elimination of H(3)PO(4) to give rise to the [M-H-98](-) fragments. The mechanism proposed for the phosphoric acid neutral loss is based on extensive CID studies of Ala-substituted model phosphorylated peptides and oxygen-18 labeling. The proposed mechanistic pathway explains the fact that the pTyr phosphate transfer and the subsequent H(3)PO(4) neutral loss are not observed for multiply charged anions of pTyr-peptides. Monoanions of pSer-containing peptides undergo the intramolecular phosphate shift as well, although its efficiency is much lower compared to the aromatic phosphorylation sites. These observations facilitate correct identification of pSer-, pThr-, and pTyr-peptides in CID studies. This work demonstrates that the established phosphate-specific neutral loss fragmentation rules of protonated pTyr-peptides cannot be applied to the CID spectra of their [M-H](-) ions.

Improved infrared multiphoton dissociation of peptides through N-terminal phosphonite derivatization

A strategy for improving the sequencing of peptides by infrared multiphoton dissociation (IRMPD) in a linear ion trap mass spectrometer is described. We have developed an N-terminal derivatization reagent, 4-methylphosphonophenylisothiocyanate (PPITC), which allows the attachment of an IR-chromogenic phosphonite group to the N-terminus of peptides, thus enhancing their IRMPD efficiencies. After the facile derivatization process, the PPITC-modified peptides require shorter irradiation times for efficient IRMPD and yield extensive series of y ions, including those of low m/z that are not detected upon traditional CID. The resulting IRMPD mass spectra afford more complete sequence coverage for both model peptides and tryptic peptides from cytochrome c. We compare the effectiveness of this derivatization/IRMPD approach to that of a common N-terminal sulfonation reaction that utilizes 4-sulfophenylisothiocyanate (SPITC) in conjunction with CID and IRMPD.

Comparison of infrared multiphoton dissociation and collision-induced dissociation of supercharged peptides in ion traps

The number and types of diagnostic ions obtained by infrared multiphoton dissociation (IRMPD) and collision-induced dissociation (CID) were evaluated for supercharged peptide ions created by electrospray ionization of solutions spiked with m-nitrobenzyl alcohol. IRMPD of supercharged peptide ions increased the sequence coverage compared with that obtained by CID for all charge states investigated. The number of diagnostic ions increased with the charge state for IRMPD; however, this trend was not consistent for CID because the supercharged ions did not always yield the greatest number of diagnostic ions. Significantly different fragmentation pathways were observed for the different charge states upon CID or IRMPD with the latter yielding far more immonium ions and often fewer uninformative ammonia, water, and phosphoric acid neutral losses. Pulsed-Q dissociation resulted in an increase in the number of internal product ions, a decrease in sequence-informative ions, and reduced overall ion abundances. The enhanced sequence coverage afforded by IRMPD of supercharged ions was demonstrated for a variety of model peptides, as well as for a tryptic digest of cytochrome c.

A mechanistic study of the electron capture dissociation of oligonucleotides

Electron capture dissociation (ECD) of a series of custom-synthesized oligonucleotide pentamers was performed in a Fourier-transform mass spectrometer with a conventional filament-type electron gun. Dissociation of oligonucleotide ions by electron capture generates primarily w/d-type and z/a-type ions with and without the loss of a nucleobase fragment ions. Minor yields of radical [z/a + H]. fragment ions were also observed in many cases. It is interesting to note that some nucleoside-like fragment ions and protonated nucleobase ions (except thymine-related nucleobases and nucleoside-like fragments) were observed in most ECD spectra. The formation of these low-mass fragment ions was tentatively attributed to the secondary fragmentation of the radical [z + H]. fragment ions. From the ECD tandem mass spectra of a series of C/T based binary oligonucleotide ions, including d(CTCTC), d(CTTTC), d(TCCCT), d(CCCCT), and d(TCCCC), it was clearly demonstrated that the formation of many sequence ions was sensitive to the position of cytosine (or the position of charge carrier). The findings of this work support a notion that the ECD of protonated oligonucleotide molecules is charge-directed with the electron being captured by the protonated nucleobase.

Infrared multiphoton dissociation mass spectrometry for structural elucidation of oligosaccharides

The structural elucidation of oligosaccharides remains a major challenge. Mass spectrometry provides a rapid and convenient method for structural elucidation on the basis of tandem mass spectrometry. Ions are commonly selected and subjected to collision-induced dissociation (CID) to obtain structural information. However, a disadvantage of CID is the decrease in both the degree and efficiency of dissociation with increasing mass. In this chapter, we illustrate the use of infrared multiphoton dissociation (IRMPD) to obtain structural information for O- and N-linked oligosaccharides. The IRMPD and CID behaviors of oligosaccharides are compared.

Towards liquid chromatography time-scale peptide sequencing and characterization of post-translational modifications in the negative-ion mode using electron detachment dissociation tandem mass spectrometry

Electron detachment dissociation (EDD) of peptide poly-anions is gentle towards post-translational modifications (PTMs) and produces predictable and interpretable fragment ion types (a., x ions). However, EDD is considered an inefficient fragmentation technique and has not yet been implemented in large-scale peptide characterization strategies. We successfully increased the EDD fragmentation efficiency (up to 9%), and demonstrate for the first time the utility of EDD-MS/MS in liquid chromatography time-scale experiments. Peptides and phosphopeptides were analyzed in both positive- and negative-ion mode using electron capture/transfer dissociation (ECD/ETD) and EDD in comparison. Using approximately 1 pmol of a BSA tryptic digest, LC-EDD-MS/MS sequenced 14 peptides (27% aa sequence coverage) and LC-ECD-MS/MS sequenced 19 peptides (39% aa sequence coverage). Seven peptides (18% aa sequence coverage) were sequenced by both EDD and ECD. The relative small overlap of identified BSA peptides demonstrates the complementarity of the two dissociation modes. Phosphopeptide mixtures from three trypsin-digested phosphoproteins were subjected to LC-EDD-MS/MS resulting in the identification of five phospho-peptides. Of those, one was not found in a previous study using a similar sample and LC-ETD-MS/MS in the positive-ion mode. In this study, the ECD fragmentation efficiency (15.7% av.) was superior to the EDD fragmentation efficiency (3.6% av.). However, given the increase in amino acid sequence coverage and extended PTM characterization the new regime of EDD in combination with other ion-electron fragmentation techniques in the positive-ion mode is a step towards a more comprehensive strategy of analysis in proteome research.

Chromogenic cross-linker for the characterization of protein structure by infrared multiphoton dissociation mass spectrometry

We have developed a new IR chromogenic cross-linker (IRCX) to aid in rapidly distinguishing cross-linked peptides from unmodified species in complex mixtures. By incorporating a phosphate functional group into the cross-linker, one can take advantage of its unique IR absorption properties, affording selective infrared multiphoton dissociation (IRMPD) of the cross-linked peptides. In a mock mixture of unmodified peptides and IRCX-cross-linked peptides (intramolecularly and intermolecularly cross-linked), only the peptides containing the IRCX modification were shown to dissociate upon exposure to 50 ms of 10.6-microm radiation. LC-IRMPD-MS proved to be an effective method to distinguish the cross-linked peptides in a tryptic digest of IRCX-cross-linked ubiquitin. A total of four intermolecular cross-links and two dead-end modifications were identified using IRCX and LC-IRMPD-MS. IRMPD of these cross-linked peptides resulted in secondary dissociation of all primary fragment ions containing the chromophore, producing a series of unmodified b- or y-type ions that allowed the cross-linked peptides to be sequenced without the need for collision-induced dissociation.

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.

Identification of protein phosphorylation sites within Ser/Thr-rich cluster domains using site-directed mutagenesis and hybrid linear quadrupole ion trap Fourier transform ion cyclotron resonance mass spectrometry

We describe a method for the analysis of multi-site phosphorylation in serine/threonine (Ser/Thr)-rich protein sequences. Site-specific mutagenesis was used to introduce tryptic cleavage sites in the serine glutamine/threonine glutamine cluster domain (SCD) of the human checkpoint protein kinase (Chk2). The mutant proteins were shown to autophosphorylate on residues that are inducibly phosphorylated when mammalian cells are exposed to ionizing radiation (serine 33/35, serine 516, threonine 68 and threonine 432). Five Ser/Thr clusters within the SCD were flanked by arginine or lysine residues to produce tryptic peptides for nanospray liquid chromatography (nanoLC)/linear quadrupole ion trap Fourier transform ion cyclotron resonance mass spectrometry. Phosphorylation sites were assigned using accurate-mass-driven analysis and interpretation of low-energy collision-induced dissociation spectra acquired in the ion trap. In addition to verifying known phosphorylation sites, seventeen novel sites were identified within the SCD of Chk2. The approach should be applicable to other O-linked post-translational modifications that occur in proteins with Ser/Thr-rich sequences.

Phosphoproteomics of human platelets: A quest for novel activation pathways

Besides their role in hemostasis, platelets are also highly involved in the pathogenesis and progression of cardiovascular diseases. Since important and initial steps of platelet activation and aggregation are regulated by phosphorylation events, a comprehensive study aimed at the characterization of phosphorylation-driven signaling cascades might lead to the identification of new target proteins for clinical research. However, it becomes increasingly evident that only a comprehensive phosphoproteomic approach may help to characterize functional protein networks and their dynamic alteration during physiological and pathophysiological processes in platelets. In this review, we discuss current methodologies in phosphoproteome research including their potentials as well as limitations, from sample preparation to classical approaches like radiolabeling and state-of-the-art mass spectrometry techniques.

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

Sequential ion/ion reactions have been used to characterize phosphopeptides present in relatively simple peptide mixtures, including one generated from the tryptic digestion of alpha-casein. The phosphopeptides in these mixtures gave rise to either low or no signals via positive ion electrospray ionization. Strong signals, however, were generated in the negative ion mode. An initial ion/ion reaction that employed multiply protonated amino-terminated dendrimers converted phosphopeptide anions to the doubly protonated species. The doubly charged cations were then subjected to ion/ion electron transfer to induce dissociation. Electron-transfer dissociation of doubly positively charged phosphopeptides yields characteristic c- and z-type fragment ions by dissociation of the N-C(alpha) bond along the peptide backbone while preserving the labile posttranslational modifications. These results illustrate the ability to alter ion charge after ion formation and prior to structural interrogation. Phosphopeptides provide an example where it can be difficult to form strong doubly charged cation signals directly when they are present in mixtures, which, as a result, precludes the use of electron-transfer dissociation as a structural probe. The sequential ion/ion reaction process described here, therefore, can provide a new capability for structural interrogation in phosphoproteomics.

Automatic determination of O-glycan structure from fragmentation spectra

Glycosylation is one of the most important classes of post-translational protein modifications, but the identification of glycans is difficult because of their branched structures and numerous isomers. We describe an algorithm called CartoonistTwo that proposes structures for O-linked glycans by automatically analyzing fragmentation mass spectra. CartoonistTwo improves upon previous glycan identification software primarily in its scoring function, which can more successfully distinguish among a number of similar structures. CartoonistTwo was designed and tested with FTICR mass spectra, and includes automatic recalibration and peak selection especially tuned for such data, yet it can be easily adapted to fragmentation spectra (MS2 or MSn) from other instrument types. On a validated test set of 34 SORI-CID MSn FTICR spectra from Xenopus egg jelly, CartoonistTwo gave the manually determined structural assignment either the first or second highest score over 90% of the time. And for over 50% of these spectra, CartoonistTwo selected a unique highest scoring structure that agreed with the manually determined one.

State-of-the-art in phosphoproteomics

Presently, phosphorylation of proteins is the most studied and best understood PTM. However, the analysis of phosphoproteins and phosphopeptides is still one of the most challenging tasks in contemporary proteome research. Since not every phosphoprotein is accessible by a certain method and identification of the phosphorylated amino acid residue is required in the majority of cases, various strategies for the detection and localization of phosphorylations have been developed. Identification and localization of protein phosphorylations is mostly done by MS nowadays but phosphoproteins and -peptides are often suppressed in comparison to the unphosphorylated species if measured in complex mixtures. Thus, the isolation of pure phosphopeptide samples is a main task. This review gives an overview over the most frequently used methods in isolation and detection of phosphoproteins and -peptides such as specific enrichment or separation strategies as well as the localization of the phosphorylated residues by various mass spectrometric techniques.

Detection of amino acid and peptide phosphate protonation using Raman spectroscopy

Raman spectra of phosphorylated amino acids and peptides undergo pH-dependent changes attributed to protonation of -OPO(3)(2-) (dibasic) to -OPO(3)H(-) (monobasic). Bands at approximately 980 and 1080cm(-1) in solution Raman spectra of phosphoserine and phosphothreonine are assigned to the monobasic and dibasic phosphate groups, respectively. Calibrated Raman peak area ratio measurements, performed as a function of pH, are used to determine the corresponding pKa values of 5.6 (phosphoserine) and 5.9 (phosphothreonine). In peptides, the phosphate Raman bands are difficult to distinguish due to interference from other neighboring bands (particularly those derived from aromatic amino acid residues) as well as the relatively low solubility of peptides. Nevertheless, drop coating deposition Raman (DCDR) spectra obtained from 100-microM peptide solutions reveal pH-dependent second derivative features at approximately 980 and 1080cm(-1), which are indicative of phosphate protonation.

Mapping sites of protein phosphorylation by mass spectrometry utilizing a chemical-enzymatic approach: characterization of products from alpha-S1 casein phosphopeptides

A novel chemical-enzymatic approach was developed to facilitate identification of phosphorylation sites in isolated phosphoproteins. ESI-TOF mass spectrometry was used to characterize products from the chemical-enzymatic cleavage of specific phosphorylation sites in bovine alpha-S1 casein and synthetic phosphopeptides containing substitutions at a single phosphorylation site. Further refinements to this approach for identification of protein phosphorylation sites and its utility for the quantification of phosphopeptides by isotope-dilution mass spectrometry are presented.