Discrimination of Aspartic and Isoaspartic Acid Residues in Peptides by Tandem Mass Spectrometry with Hydrogen Attachment Dissociation.

Long-lived proteins undergo chemical modifications that can cause age-related diseases. Among these chemical modifications, isomerization is the most difficult to identify. Isomerization often occurs at the aspartic acid (Asp) residues. In this study, we used tandem mass spectrometry equipped with a newly developed ion activation method, hydrogen attachment dissociation (HAD), to analyze peptides containing Asp isomers. Although HAD preferentially produces [cn + 2H]+ and [zm + 2H]+ via N-Cα bond cleavage, [cn + 58 + 2H]+ and [zm - 58 + 2H]+ originate from the fragmentation of the isoAsp residue. Notably, [cn + 58 + 2H]+ and [zm - 58 + 2H]+ could be used as diagnostic fragment ions for the isoAsp residue because these fragment ions did not originate from the Asp residue. The detailed fragmentation mechanism was investigated by computational analysis using density functional theory. According to the results, hydrogen attachment to the carbonyl oxygen in the isoAsp residue results in the Cα-Cß bond cleavage. The experimental and theoretical joint study indicates that the present method allows us to discriminate Asp and isoAsp residues, including site identification of the isoAsp residue. Moreover, we demonstrated that the molar ratio of peptide isomers in the mixture could be estimated from their fragment ion abundance. Therefore, tandem mass spectrometry with HAD is a useful method for the rapid discrimination and semiquantitative analysis of peptides containing isoAsp residues.

Tuning the Internal Energy of Ions Produced by Atmospheric and High-Pressure Electrospray by Modulating the Gas Throughput into the First Vacuum Stage.

In a high-pressure environment, electrospray ionization (ESI) can be achieved without discharge between the emitter and the counter electrode, thus enabling the generation of gas-phase ions from liquid with high surface tension, such as pure water, which requires a high onset voltage for stable ESI. In this study, the ion dissociation during the transferring of ions/charged droplets from a superatmospheric pressure environment to vacuum has been systematically investigated using benzyl ammonium thermometer ions. The ion source pressure did not affect the internal energy distribution of ions, whereas the gas throughput into the first vacuum stage clearly influences the internal energy distribution of the ions. The increase in the gas throughput increased the density of molecules/atoms presented in ion transfer/focusing electrodes located in the first vacuum stage. As a result, the mean free path of ions in the first vacuum stage decreases, and the energy of ions decreases by decreasing the kinetic energy involved in each collision between ions and residue gas. The gas throughput into the first vacuum stage is found to describe the internal energy distribution of ions associated with the local conditions more quantitatively instead of using the measured pressure of the vacuum stage, which is different from the effective local pressure. This study also demonstrated the controlled dissociation of ions using the ion transfer settings of the instrument in combination with ion inlet tubes of different sizes.

Predictive Value of Vancomycin AUC24/MIC Ratio for 30-day Mortality in Patients with Severe or Complicated Methicillin-Resistant Staphylococcus aureus Infections: A Multicenter Retrospective Study.

BACKGROUND: Although vancomycin is typically employed against methicillin-resistant Staphylococcus aureus (MRSA) infections, the optimal ratio of 24-h area under the concentration-time curve to minimum inhibitory concentration (AUC24/MIC) for severe or complicated infections lacks clear guideline recommendations. This study aimed to determine the target AUC24/MIC ratio associated with treatment outcomes of infections treated with vancomycin. METHODS: This retrospective multicenter cohort study included adult patients receiving ≥ 5 days of vancomycin for severe/complicated MRSA infections (e.g., osteoarticular, pulmonary, endocarditis, etc.) between January 2018 and December 2023. The primary outcome was 30-day mortality, with secondary outcomes including clinical success, microbiological eradication, and nephrotoxicity. Receiver operating characteristic (ROC) curve analysis was used to identify the AUC24/MIC cutoff for 30-day mortality. Multivariate regression analysis was used to determine association between AUC24/MIC and outcomes. RESULTS: This study included 82 patients. ROC identified a target AUC24/MIC of ≥ 505 for 30-day mortality. The overall 30-day mortality rate (22.0%) was significantly higher for below average AUC24/MIC cutoff (34.1%) than for above AUC24/MIC cutoff group (9.8%). Multivariate analysis confirmed AUC24/MIC of < 505 as an independent predictor (adjusted odds ratio, 5.001; 95% confidence interval, 1.335-18.75). The clinical success rate differed significantly between below- and above-cutoff groups, whereas microbiological eradication tended to favor the above-cutoff group. The nephrotoxicity rates were comparable between groups. CONCLUSIONS: In treating severe/complicated MRSA infections, vancomycin AUC24/MIC ratio ≥ 505 was independently associated with favorable 30-day mortality. Given the retrospective nature of this study, further prospective studies are essential to confirm the reliability of the target AUC24/MIC ratios.

Potential risk factors for early acute kidney injury in patients treated with vancomycin.

PURPOSE: The acute kidney injury (AKI) onset owing to vancomycin (VCM) is reported that depend on the area under the blood concentration-time curve (AUC) and occur comparison early phase (early AKI). This study aimed to investigate the occurrence of early AKI in patients treated with VCM and new indicators to avoid early AKI. METHODS: Adult patients who received VCM treatment for more than 4 days and whose trough values measured at least once on or after day 4 and serum creatinine before day 7 from the initiation of VCM administration between August 2021 and September 2022 at the Yamanashi Prefectural Central Hospital were enrolled. Early AKI (defined as AKI occurring within day 7 from VCM administration) and the association between each AUC (0-24, 24-48, 48-72, 0-48, 24-72, 0-72) were investigated. Furthermore, each AUC cut-off value for early AKI was calculated. RESULT: In total, 164 patients were enrolled; early AKI developed in 21 patients and most frequently occurred on day 4. All stratified AUC were associated with early AKI development. The AUC cut-off values were AUC0-24: 470.8 µg/mL⋅h; AUC24-48: 473.0 µg/mL⋅h; AUC48-72: 489.7 µg/mL⋅h; AUC0-48: 910.2 µg/mL⋅h; AUC24-72: 1039.2 µg/mL⋅h; and AUC0-72: 1544.0 µg/mL⋅h. CONCLUSION: The possibility of AKI development owing to the AUC accumulation of VCM was observed (accumulation toxicity). Concentration control through early-phase blood concentration measurements and a transition to AUC0-48 <910.2 µg/mL⋅h may reduce the early-phase AKI onset.

Hot Hydrogen Atom Irradiation of Protonated/Deprotonated Peptide in an Ion Trap Facilitates Fragmentation through Heated Radical Formation.

Tandem mass spectrometry with fragmentation involving the reaction with hydrogen atoms is expected to be useful for the analysis of peptides and proteins. In general, hydrogen atoms preferentially react with odd-electron radicals. The attachment of hydrogen atoms to even-electron peptide ions is barely observed because of their low reaction rate. To date, only the methodology developed by our group has successfully induced the fragmentation of even-electron peptide ions by reacting with hydrogen atoms. In the present study, we focused on the temperature of the peptide ions and hydrogen atoms in an ion trap mass spectrometer to understand the mechanism of the corresponding reaction. Because the reaction between even-electron peptide ions and hydrogen atoms has a significant transition state barrier, the use of hot hydrogen atoms is required to initiate the reaction. The reaction contributes to increase the internal energy of the resultant peptide radicals because the heat of reaction and kinetic energy of the hydrogen atom are converted to the internal energy of the product. The resultant oxygen- and carbon-centered peptide radicals undergo radical-induced fragmentation with sub-picosecond and sub-millisecond time scales, respectively.

Fragmentation study of tryptophan-derived metabolites induced by electrospray ionization mass spectrometry for highly sensitive analysis.

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is interfaced with electrospray ionization (ESI), which generally produces intact gas-phase ions of biomolecules. However, ESI induces the fragmentation of tryptophan-derived metabolites, which are known to act as neurotransmitters and psychoactive drugs. Tryptophan-derived metabolites undergo N-Cα bond dissociation during ESI, producing a fragment ion with a spiro[cyclopropane-indolium] backbone. Fragmentation is suppressed by the presence of an α-carboxyl group and the modification of amino groups. In particular, tryptamine and serotonin, which lack such functional groups, produce more intense fragment-ion signals than protonated molecules. The multiple reaction monitoring (MRM)-based quantitative analysis of tryptamine and serotonin used the fragment ions produced from in-source collision-induced dissociation as the precursor ions, which improved the signal-to-noise ratio of the resulting spectra. The present method allows for the quantitative analysis of tryptamine and serotonin with high sensitivity.

Rapid chiral discrimination of oncometabolite dl-2-hydroxyglutaric acid using derivatization and field asymmetric waveform ion mobility spectrometry/mass spectrometry.

2-Hydroxyglutaric acid is a chiral metabolite whose enantiomers specifically accumulate in different diseases. An enantiomeric excess of the d-form in biological specimens reflects the existence of various pathogenic mutations in cancer patients, however, conventional methods using gas or liquid chromatography and capillary electrophoresis had not been used for large clinical studies because they require multiple analytical instruments and a long run time to separate the enantiomers. Here, we present a rapid separation method for dl-2-hydroxyglutaric acid using a chiral derivatizing reagent and field asymmetric waveform ion mobility spectrometry/mass spectrometry, which requires a single analytical instrument and <1 s for the separation. We compared three derivatization methods and found that a method using (S)-1-(4,6-dimethoxy-1,3,5-triazin-2-yl)pyrrolidin-3-amine enables the separation. In addition, we were able to detect dl-2-hydroxyglutaric acid in standard solution at lower concentrations than that previously reported for the serum. These results show the potential of the method to be used in clinical analysis.

In-Source Fragmentation of Phenethylamines by Electrospray Ionization Mass Spectrometry: Toward Highly Sensitive Quantitative Analysis of Monoamine Neurotransmitters.

Electrospray ionization mass spectrometry (ESI-MS) is widely used to analyze biomolecules, which are usually detected as protonated and cation-adducted molecules in the positive-ion mode. However, phenethylamine derivatives, which are known as neurotransmitters and psychoactive drugs, undergo the protonation and subsequently lose NH3 during ESI. As a result, intense fragment-ion signals are observed in their ESI-MS spectra, which hamper the unambiguous identification of phenethylamine derivatives. To understand the mechanism of the loss of NH3 from these phenethylammoniums, the fragmentations of model 4-substituted phenethylamines were investigated and the fragment ions were identified as spiro[2.5]octadienyliums. Fragmentation was enhanced by the presence of electron-donating groups, and most substituted phenethylamines generated spiro[2.5]octadienyliums as fragment ions during ESI-MS, except those with strong electron-withdrawing groups. The quantitative analysis of phenethylamines by liquid chromatography tandem mass spectrometry is typically performed by multiple reaction monitoring using protonated molecules as the precursor. In contrast, the conversion of precursor ions from the protonated molecules into the spiro[2.5]octadienylium fragment improved the signal-to-noise ratio, allowing the quantitative analysis of phenethylamines with high sensitivity and accuracy.

Gas-Phase Peptide Fragmentation Induced by Hydrogen Attachment, from Principle to Sequencing of Amide Nitrogen-Methylated Peptides.

Tandem mass spectrometry (MS/MS) with radical-based fragmentation was developed recently, which involves the reaction of hydrogen atoms and peptides in a process called hydrogen attachment/abstraction dissociation (HAD). HAD mainly produces [cn + 2H]+ and [zm + 2H]+ via hydrogen attachment to the carbonyl oxygen on the peptide backbone. In addition, HAD often generates [an + 2H]+ and [xm + 2H]+. To explain the formation of [an + 2H]+ and [xm + 2H]+, hydrogen attachment to the carbonyl carbon atom on the peptide backbone is proposed to initiate Cα-C bond cleavage. The resultant hydrogen-abundant oxygen-centered radical intermediate undergoes radical-induced dissociation to give [an + H]+• and [xm + 2H]+. Subsequently, [an + 2H]+ was produced by the reaction of [an + H]+• and a hydrogen atom. The fragment ions formed by the cleavage of N-Cα and Cα-C bonds are observed in the HAD-MS/MS spectra, and the mass differences of these fragment ions correspond to the mass of peptide bonds. Consequently, HAD-MS/MS allows the identification of post-translational modifications on the peptide backbone. In addition, HAD-MS/MS provides a consecutive series of [cn + 2H]+ and [an + 2H]+ as the N-terminal fragments, as well as [zm + 2H]+ and [xm + 2H]+, which enables the sequencing of peptides with post-translational modification, including the discrimination of modifications on the side chain and backbone.

Mass Spectrometric Characterization of the Partial Oxidation Process of a Gasoline Surrogate Induced by a Dielectric Barrier Discharge.

Plasma-assisted combustion can improve the thermal efficiency and stability of internal combustion engines; based on this, among various types of discharge method, surface dielectric barrier discharge (SDBD) induced partial oxidation of hydrocarbons was investigated in this study. To demonstrate the general mechanisms of SDBD-induced partial oxidation of gasoline, we used a five-component gasoline surrogate (S5R), which consisted of a mixture of alkanes (isooctane, n-heptane, and methylcyclohexane), alkenes (trimethyl pentene isomers), and toluene, as the model. The detailed process of SDBD-induced partial oxidation of hydrocarbon was investigated by Fourier transform infrared spectroscopy, ion attachment mass spectrometry, and density functional theory calculation. SDBD irradiation of the hydrocarbon/air mixture induced dissociation of oxygen molecule through direct electron impact and collision with excited nitrogen molecules, and the resultant oxygen atom then reacted with a hydrocarbon molecule. Alkane and toluene were converted to alkyl hydroperoxide by a reaction with the oxygen atom and subsequent attachment of O2. The resultant alkyl hydroperoxide then provided a ketone and/or aldehyde. In contrast, the alkenes underwent attachment of an oxygen atom and were either converted to fragments containing a carbonyl group or to etoposide. Regarding the analytical method, the partially oxidized products were selectively ionized from the hydrocarbon/air mixture when Na+ was used as the reagent ion for ion attachment mass spectrometry.

Sequencing of Sulfopeptides Using Negative-Ion Tandem Mass Spectrometry with Hydrogen Attachment/Abstraction Dissociation.

Tandem mass spectrometry (MS/MS) with radical-based fragmentation involving the attachment or abstraction of hydrogen to peptides, in a process called hydrogen attachment/abstraction dissociation (HAD), has been recently developed. HAD-MS/MS is considered a useful method for the analysis of proteins with post-translational modification (PTM) because of its ability to determine the PTM site on proteins. In the present investigation, we analyzed highly acidic sulfopeptides and sulfoprotein digests using negative-ion HAD-MS/MS combined with matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI). In general, MALDI and ESI produced singly and multiply charged peptides, respectively. HAD of singly deprotonated sulfopeptides preferentially produced fragment ions with sulfonation, whereas both sulfonated and nonsulfonated fragment ions were observed in the HAD-MS/MS spectrum of multiply deprotonated sulfopeptides. A comparison of the MALDI and ESI HAD-MS/MS spectra allows the discrimination of sulfonated and nonsulfonated fragments, which would be helpful in performing de novo sequencing of sulfopeptides. In addition, the combination of ESI-based HAD-MS/MS and liquid chromatography (LC) allows the analysis of sulfopeptides present in protein digests. LC-ESI-MS/MS with HAD is a potentially useful method for sulfoproteomic application.

Hydrogen atom attachment to histidine and tryptophan containing peptides in the gas phase.

In this study, we use a combination of tandem mass spectrometry and hydrogen radical-mediated fragmentation techniques to analyze the sequence of peptides. We focus on fragmentation induced by the attachment of hydrogen atoms to the histidine and tryptophan residue side-chains in the peptide that occurs in the gas-phase. The hydrogen atom attached to the imidazole and indole rings in the histidine and tryptophan residues, respectively, and the resulting intermediate experienced Cα-Cß bond cleavage. The detailed fragmentation mechanism is investigated by computational analysis using density functional theory. According to the results, hydrogen attachment occurs at the C-5 position in histidine and at the C-2 position in the tryptophan, which has a lower activation energy compared with the other positions and the resulting intermediate radicals yielded fragments due to Cα-Cß bond cleavage. For the peptides that contain the histidine and tryptophan residues, cleavages in the Cα-Cß and N-Cα bonds occurred independently. Therefore, the method presented in this study is applicable when analyzing peptides that contain histidine and tryptophan residues.

Hydrogen attachment dissociation of peptides containing disulfide bonds.

A combination of tandem mass spectrometry (MS/MS) and hydrogen attachment dissociation (HAD) is a useful method for peptide sequence analysis. In this study, gas-phase fragmentation induced by the attachment of hydrogen to peptides containing disulfide bonds was investigated. Hydrogen attachment induced the cleavage of either the disulfide or N-Cα bond, which competitively occurred during HAD. The disulfide bond cleavage proceeded through an intermediate, which contains a thiyl radical (-S˙) and a thiol group (-SH). In contrast, N-Cα bond cleavage produced an intermediate containing an enol-imine group and α-carbon radical. The intermediate α-carbon radical then attacked the disulfide bond, resulting in a cyclic [z]+ fragment. The counterpart, [c + H]+˙ with a thiyl radical underwent further hydrogen attachment, producing [c + 2H]+. Because both disulfide and N-Cα bonds were cleaved by a single hydrogen attachment event, HAD-MS/MS can provide sequence information for the backbone region in the disulfide loop.

De Novo Sequencing of Tryptic Phosphopeptides Using Matrix-Assisted Laser Desorption/Ionization Based Tandem Mass Spectrometry with Hydrogen Atom Attachment.

Phosphorylation is the most abundant protein modification, and tandem mass spectrometry (MS/MS) with radical-based fragmentation techniques has proven to be a promising method for phosphoproteomic applications, owing to its ability to determine phosphorylation sites on proteins. The radical-induced fragmentation technique involves the attachment or abstraction of hydrogen to peptides in an ion trap mass spectrometer, in a process called hydrogen attachment/abstraction dissociation (HAD), which has only been recently developed. In the present investigation, we have analyzed model phosphopeptides and phosphoprotein digests using HAD-MS/MS, combined with matrix-assisted laser desorption/ionization (MALDI), in order to demonstrate the usefulness of the HAD-MS/MS-based analytical method. The tryptic peptides were categorized as arginine- and lysine-terminated peptides, and MALDI HAD-MS/MS is found to facilitate the sequencing of arginine-terminated tryptic peptides, because of the selective observation of C-terminal side fragment ions. In contrast, MALDI HAD-MS/MS of lysine-terminated tryptic peptides produced both N- and C-terminal side fragments, such that the mass spectra were complex. The guanidination of peptide converted lysine into homoarginine, which facilitated the interpretation of MALDI HAD-MS/MS mass spectra. The present method was useful for de novo sequencing of tryptic phosphopeptides.

Structural Analysis of Phospholipid Using Hydrogen Abstraction Dissociation and Oxygen Attachment Dissociation in Tandem Mass Spectrometry.

Gas-phase hydrogen radicals were introduced into a quadrupole ion trap containing singly charged phospholipids to obtain structural fragmentation patterns in tandem mass spectrometry (MS/MS). Saturated and unsaturated phosphatidylcholines were used as a model phospholipid, whose chain-length ranges between 16 and 24. The MS/MS spectrum yielded a continuous series of fragment ions with a mass difference of 14 Da, representing the saturated fatty acyl chains. The fragment ions corresponding to the double-bond position within a single fatty acyl chain showed a characteristic mass difference of 12 Da. The detection of these diagnostic product ions enabled the structural analysis of double-bond isomers of phospholipids. To further investigate the potential of radical-induced dissociation for the isomeric analysis of phospholipids, gas-phase hydroxyl radicals, and triplet oxygen atoms were employed in tandem mass spectrometry. The methylene bridges adjacent to the double-bond positions were selectively dissociated, accompanied by oxidation of the double bonds. Tandem mass spectrometry incorporating multiple radical species facilitates the structural analysis of isomeric phospholipids.

Influence of the metals and ligands in dinuclear complexes on phosphopeptide sequencing by electron-transfer dissociation tandem mass spectrometry.

Phosphorylation is one of the most important protein modifications, and electron-transfer dissociation tandem mass spectrometry (ETD-MS/MS) is a potentially useful method for the sequencing of phosphopeptides, including determination of the phosphorylation site. Notably, ETD-MS/MS typically provides useful information when the precursor contains more than three positive charges. It is not yet used as an analysis method for large-scale phosphopeptide production due to difficulties occurring in the production of acidic phosphopeptides having more than three positive charges. To increase the charge state of phosphopeptides, we used dinuclear metal complexes, which selectively bind to the phosphate group in phosphopeptides with the addition of positive charge(s). Dinuclear copper, zinc, and gallium complexes were tested and it was found that the type of metal present in the complex strongly affected the affinity of the phosphorylated compounds and their ETD fragmentation. The dinuclear copper complex interacted weakly with the phosphate groups and ETD-induced peptide fragmentation was largely suppressed by the presence of Cu2+, which worked as an electron trap. The dinuclear gallium complex was strongly bound to a phosphate group. However, the ligand binding to gallium acted as an electron trap and the presence of dinuclear gallium complex in the precursor for ETD-MS/MS hampered the sequencing of the phosphopeptides, as in the case of dinuclear copper complexes. In contrast, dinuclear zinc complexes efficiently bind to phosphopeptides with an increase in the charge state, facilitating phosphopeptide sequencing by ETD-MS/MS. The fragmentation of the ligand and peptide backbone in the dinuclear zinc-phosphopeptide complex were competitively induced by ETD. These processes are influenced by the ligand structure and so the detailed ETD fragmentation pathways were investigated using density functional theory calculations.

Real-time monitoring for reforming processes of liquid hydrocarbon fuel-air pre-mixtures by non-thermal plasmas using ion attachment mass spectrometry.

Plasma induced reforming processes of fuel-air mixtures were investigated to understand the mechanism of the plasma-assisted combustion technique, which can improve the thermal efficiency and stability of internal combustion engines. In this study, a mixture of air with isooctane or n-heptane fuels was reformed by non-thermal plasma in a flow reactor, generated by a dielectric barrier discharge, and then directly analyzed using ion attachment mass spectrometry. Plasma irradiation of an air/hydrocarbon mixture produced an oxygen atom which then reacted with a hydrocarbon, leading to hydroxyl and alkyl radicals. The alkyl radical was immediately converted to alkyl hydroperoxide, which is suggested to be a long-living intermediate for the fuel reforming process. Finally, ketone and aldehyde were formed through the alkyloxy radical intermediate. The details of each reaction process were investigated by ab initio calculations. The proposed plasma induced fuel reforming processes are strongly supported by the computational results.

Fundamental study of hydrogen-attachment-induced peptide fragmentation occurring in the gas phase and during the matrix-assisted laser desorption/ionization process.

Mass spectrometry with hydrogen-radical-mediated fragmentation techniques has been used for the sequencing of proteins/peptides. The two methods, matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) and hydrogen attachment/abstraction dissociation (HAD) are known as hydrogen-radical-mediated fragmentation techniques. MALDI-ISD occurs during laser induced desorption processes, whereas HAD utilizes the association of hydrogen with peptide ions in the gas phase. In this study, the general mechanisms of MALDI-ISD and HAD of peptides were investigated. We demonstrated the fragmentation of four model peptides and investigated the fragment formation pathways using density functional theory (DFT) calculations. The current experimental and computational joint study indicated that MALDI-ISD and HAD produce aminoketyl radical intermediates, which immediately undergo radical-induced cleavage at the N-Cα bond located on the C-terminal side of the radical site, leading to the c'/z˙ fragment pair. In the case of MALDI-ISD, the z˙ fragments undergo a subsequent reaction with the matrix to give z' and matrix adducts of the z fragments. In contrast, the c' and z˙ fragments react with hydrogen atoms during the HAD processes, and various fragment species, such as c˙, c', z˙ and z', were observed in the HAD-MS/MS mass spectra.

Principles of hydrogen radical mediated peptide/protein fragmentation during matrix-assisted laser desorption/ionization mass spectrometry.

Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) is a very easy way to obtain large sequence tags and, thereby, reliable identification of peptides and proteins. Recently discovered new matrices have enhanced the MALDI-ISD yield and opened new research avenues. The use of reducing and oxidizing matrices for MALDI-ISD of peptides and proteins favors the production of fragmentation pathways involving "hydrogen-abundant" and "hydrogen-deficient" radical precursors, respectively. Since an oxidizing matrix provides information on peptide/protein sequences complementary to that obtained with a reducing matrix, MALDI-ISD employing both reducing and oxidizing matrices is a potentially useful strategy for de novo peptide sequencing. Moreover, a pseudo-MS(3) method provides sequence information about N- and C-terminus extremities in proteins and allows N- and C-terminal side fragments to be discriminated within the complex MALDI-ISD mass spectrum. The combination of high mass resolution of a Fourier transform-ion cyclotron resonance (FTICR) analyzer and the software suitable for MALDI-ISD facilitates the interpretation of MALDI-ISD mass spectra. A deeper understanding of the MALDI-ISD process is necessary to fully exploit this method. Thus, this review focuses first on the mechanisms underlying MALDI-ISD processes, followed by a discussion of MALDI-ISD applications in the field of proteomics. © 2014 Wiley Periodicals, Inc., Mass Spec Rev 35:535-556, 2016.

High-Confidence Sequencing of Phosphopeptides by Electron Transfer Dissociation Mass Spectrometry Using Dinuclear Zinc(II) Complex.

Phosphorylation is the most abundant protein modification, and tandem mass spectrometry (MS2) with electron transfer dissociation (ETD) has proven to be a promising method for phosphoproteomic applications owing to its ability to determine phosphorylation sites on proteins. However, low precursor charge states hinder the ability to obtain useful information through peptide sequencing by ETD, and the presence of acidic phosphate groups contributes to a low charge state of peptide ions. In the present report, we used a dinuclear zinc complex, (Zn2L)3+ (L = alkoxide form of 1,3-bis[bis(pyridin-2-ylmethyl)amino]propan-2-ol) for electrospray ionization (ESI), followed by ETD-MS2 analysis. Since (Zn2L)3+ selectively bound to phosphopeptide with addition of a positive charge per phosphate group, the use of (Zn2L)3+ for ESI improved the ionization yield of phosphopeptides in phosphoprotein digest. Additionally, an increase in the charge state of phosphopeptides were observed by addition of (Zn2L)3+, facilitating phosphopeptide sequencing by ETD-MS2. Since the binding between (Zn2L)3+ and the phosphate group was retained during the ETD process, a comparison between the ETD mass spectra obtained using two dinuclear zinc complex derivatives containing different zinc isotopes, namely (64Zn2L)3+ and (68Zn2L)3+, provided information about the number of phosphate groups in each fragment ion, allowing the phosphorylation site to be unambiguously determined. The details of the fragmentation processes of the (Zn2L)3+-phosphopeptide complex were investigated using a density functional theory calculation. As in the case of protonated peptides, ETD induced peptide backbone dissociation in the (Zn2L)3+-phosphopeptide complex proceeded through an aminoketyl radical intermediate.