Collision-induced Dissociation Modes Research Articles

Identification and analytical characterization of N-propyl norbutylone, N-butyl norbutylone, N-benzyl norheptedrone, and N-pyrrolidinyl-3,4-DMA.

In this study, the analytical characterization of three cathinones and one N-pyrrolidinyl-substituted amphetamine derivative is described: 1-([3,4-methylenedioxyphenyl])-2-(propylamino)butan-1-one (N-propyl norbutylone 1), 1-([3,4-methylenedioxyphenyl])-2-(butylamino)butan-1-one (N-butyl norbutylone 2), 2-(benzylamino)-1-phenylheptan-1-one (N-benzyl norheptedrone 3), and 1-(1-[3,4-dimethoxyphenyl]propan-2-yl)pyrrolidine (N-pyrrolidinyl-3,4-DMA 4). The identification was based on ultra-high-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry (UHPLC-QTOF-MS), gas chromatography-orbitrap MS (GC-Orbitrap-MS), nuclear magnetic resonance spectroscopy (NMR), and Fourier transform infrared (FT-IR). GC-Orbitrap-MS, with higher mass accuracy, benefit more on the accurate structure elucidation of product ions compared with the low-resolution GC-MS. The collision-induced dissociation (CID) and electron ionization (EI) pathways of these compounds were examined to assist forensic laboratories in elucidating the structure of new psychoactive substances (NPS) with similar structure in their case work. In addition, electron activated dissociation (EAD) was applied to analyze N-benzyl norheptedrone, which showed only one product ion in the CID mode. The result showed that for compound with limited product ions in the CID mode, the EAD mode can give more complementary information for structure elucidation. In addition, quantitative NMR (qNMR) was applied for the quantification of four powdered/crystal and two herbal blend seized samples. To our knowledge, no analytical data about the compounds 3 and 4 have appeared until now, making this the first report on these compounds.

Identification of New Psychoactive Tryptamines 4-OH-MET and 4-AcO-DMT Using High Resolution Mass Spectrometry and Nuclear Magnetic Resonance Spectroscopy

Objective To detect the uncontrolled new psychoactive tryptamines involved in drug-related cases with high resolution mass spectrometry and nuclear magnetic resonance spectroscopy. Methods White and brown powder obtained in actual cases were extracted and analyzed by gas chromatography-quadrupole time-of-flight mass spectrometry （GC-QTOF-MS）, ultra-high performance liquid chromatography-linear ion trap quadrupole-orbitrap mass spectrometry （UPLC-LTQ-Orbitrap MS） and 1H-nuclear magnetic resonance spectroscopy （1H-NMR）. Results After detection by GC-QTOF-MS, the components of white powder showed main characteristic fragment ion peaks at m/z 218.141 0 （molecular ion peak）, 72.080 6 （base peak）, etc. After detection by UPLC-LTQ-Orbitrap MS, its protonated molecular ion was m/z 219.149 4. The main ions in the secondary mass spectrum under the collision-induced dissociation （CID） mode were m/z 160.076 3 and 72.080 8. After detection by GC-QTOF-MS, the components of brown powder showed main characteristic fragment ion peaks at m/z 246.135 7 （molecular ion peak）, 58.065 1 （base peak）, etc. After detection by UPLC-LTQ-Orbitrap MS, its protonated molecular ion was m/z 247.145 0. The main ions in the secondary mass spectrum under CID mode were m/z 202.087 1, 160.076 3 and 134.060 5. NIST 17 library retrieval and 1H-NMR confirmed that the white powder and brown powder contained new psychoactive tryptamines 4-OH-MET and 4-AcO-DMT, respectively. Conclusion GC-QTOF-MS, UPLC-LTQ-Orbitrap MS and 1H-NMR can be used together to identify unknown new psychoactive substances.

Mass Spectral Character of Fentanyl Analogues.

Objective To provide the reference for the identification of unknown fentanyl analogues by studying the characteristic ions and main fragmentation pathways of fentanyl analogues in the modes of collision induced dissociation （CID） and electron ionization （EI）. Methods Nine fentanyl analogues （2, 2'-difluorofentanyl, acetyl fentanyl, fentanyl, butyl fentanyl, valeryl fentanyl, acryloyl fentanyl, furan fentanyl, 4-fluorine isobutyl fentanyl, carfentanyl） were selected and analyzed with ultra-high performance liquid chromatography-quadrupole time-of-flight-mass spectrometry （UHPLC-QTOF-MS） and gas chromatography-mass spectrometry （GC-MS）. The mass spectrum obtained was analyzed. The CID and EI fragmentation routes of fentanyl analogues were speculated. Results The CID and EI fragmentation pathways were highly similar. In the CID mode, characteristic ions were formed by the carbon-nitrogen bond cleavage between the piperidine ring and the N-phenyl-amide moiety, within the piperidine ring, and between the phenethyl and piperidine ring. While in the EI mode, dissociation of the piperidine ring, as well as cleavage between the piperidine ring and the phenethyl were the main fragmentation pathways. Conclusion This study summarizes the main fragmentation pathways and characteristic ions of fentanyl analogues in the CID and EI modes, which is useful for forensic laboratories to identify and structural analyze fentanyl type new psychoactive substance in practical work.

Negative Ion Mode Collision-Induced Dissociation for Analysis of Protein Arginine Methylation

Arginine methylation is a common protein post-translational modification (PTM) that plays a key role in eukaryotic cells. Three distinct types of this modification are found in mammals: asymmetric Nη1Nη1-dimethylarginine (aDMA), symmetric Nη1Nη2-dimethylarginine (sDMA), and an intermediate Nη1-monomethylarginine (MMA). Elucidation of regulatory mechanisms of arginine methylation in living organisms requires precise information on both the type of the modified residues and their location inside the protein amino acid sequences. Despite mass spectrometry (MS) being the method of choice for analysis of multiple protein PTMs, unambiguous characterization of protein arginine methylation may not be always straightforward. Indeed, frequent internal basic residues of Arg methylated tryptic peptides hamper their sequencing under positive ion mode collision-induced dissociation (CID), the standardly used tandem mass spectrometry method, while the relative stability of the aDMA and sDMA side chains under alternative non-ergodic electron-based fragmentation techniques, electron-capture and electron transfer dissociations (ECD and ETD), may impede differentiation between the isobaric residues. Here, for the first time, we demonstrate the potential of the negative ion mode collision-induced dissociation MS for analysis of protein arginine methylation and present data revealing that the negative polarity approach can deliver both an unambiguous identification of the arginine methylation type and extensive information on the modified peptide sequences.

Malonylginsenosides with Potential Antidiabetic Activities from the Flower Buds of Panax ginseng.

LC-MS-guided phytochemical isolation of malonylginsenosides, featuring neutral elimination of CO2 and C3H2O3 by the negative mode collision-induced dissociation, from the flower buds of Panax ginseng led to the isolation of 19 malonyl-substituted triterpenoid saponins. They include 15 new malonylginsenosides, malonylfloralginsenosides-Re1-Re3 (1-3), -Rb1 and -Rb2 (4, 5), -Rd1-Rd6 (6-11), and -Rc1-Rc4 (12-15), and the known m-Rb1, m-Rc, m-Rb2, and m-Rd (16-19). Compound 11 represents the first dimalonyl saponin isolated from the Panax genus, while 2-4, 9, and 10 are five ginsenosides with single malonylation at the C-20 sugar chain. The antidiabetic activities of nine of these malonyl-substituted ginsenosides (1, 3, 4, 8, 13, and 16-19) and five of the corresponding non-malonyl ginsenosides (Re, Rb1, Rb2, Rc, and Rd) were evaluated by L6 myotubes' glucose consumption and AMPKα2β1γ1 activation. Ginsenoside Rb2, 1, and 18 promoted glucose consumption of differentiated L6 myotubes, while ginsenosides Rb1, Rb2, and Rd and the malonylginsenosides 4, 8, 13, 16, 17, and 19 activated AMPKα2β1γ1 (EC50: 0.0168-2.8 μM, fold: 1.7-4.7).

Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation.

We describe a strategy for de novo peptide sequencing based on matched pairs of tandem mass spectra (MS/MS) obtained by collision induced dissociation (CID) and 351 nm ultraviolet photodissociation (UVPD). Each precursor ion is isolated twice with the mass spectrometer switching between CID and UVPD activation modes to obtain a complementary MS/MS pair. To interpret these paired spectra, we modified the UVnovo de novo sequencing software to automatically learn from and interpret fragmentation spectra, provided a representative set of training data. This machine learning procedure, using random forests, synthesizes information from one or multiple complementary spectra, such as the CID/UVPD pairs, into peptide fragmentation site predictions. In doing so, the burden of fragmentation model definition shifts from programmer to machine and opens up the model parameter space for inclusion of nonobvious features and interactions. This spectral synthesis also serves to transform distinct types of spectra into a common representation for subsequent activation-independent processing steps. Then, independent from precursor activation constraints, UVnovo's de novo sequencing procedure generates and scores sequence candidates for each precursor. We demonstrate the combined experimental and computational approach for de novo sequencing using whole cell E. coli lysate. In benchmarks on the CID/UVPD data, UVnovo assigned correct full-length sequences to 83% of the spectral pairs of doubly charged ions with high-confidence database identifications. Considering only top-ranked de novo predictions, 70% of the pairs were deciphered correctly. This de novo sequencing performance exceeds that of PEAKS and PepNovo on the CID spectra and that of UVnovo on CID or UVPD spectra alone. As presented here, the methods for paired CID/UVPD spectral acquisition and interpretation constitute a powerful workflow for high-throughput and accurate de novo peptide sequencing.

New monoterpenoid oxindole alkaloid derivatives from the stems of Uncaria hirsuta Havil. and their cytotoxicity and tandem mass spectrometric fragmentation

Four new alkaloids, comprising three 3-oxo-3,7-seco-oxindole alkaloids (hirsutanine D–F, 1–3) and one oxindole alkaloid N-oxide (uncarine B N-oxide, 4), together with four known heteroyohimbine-type oxindole alkaloids, were isolated from the stems of Uncaria hirsuta Havil. Structures of 1–4 were elucidated by extensive NMR and HR-ESIMS data analyses. Compound 3 is the first 3-oxo-3,7-seco-oxindole alkaloid with ring B opened and degraded isolated from the Uncaria genus. Compounds 1–3 exhibited slight inhibition effect on the proliferation of the breast cancer cell MDA-MB-231. The positive mode collision-induced dissociation of the 3-oxo-3,7-seco-oxindole alkaloids (1–3) was featured by the β-cleavage and α-cleavage of the amido bond, while the N-oxide (4) showed characteristic neutral eliminations of ·OH and H2O.

Identification of five pyrrolidinyl substituted cathinones and the collision‐induced dissociation of electrospray‐generated pyrrolidinyl substituted cathinones

This article reports on the analytical properties of five pyrrolidinyl substituted cathinones: α-pyrrolidinononaphenone (α-PNP, 1), 4-chloro-α-pyrrolidinopropiophenone (4-Cl-α-PPP, 2), 4-chloro-α-pyrrolidinovalerophenone (4-Cl-α-PVP, 3), 5-dihydrobenzofuranpyrovalerone (5-DBFPV, 4), and 2-(pyrrolidin-1-yl)-1-(5,6,7,8-tetrahydronaphthalen-2-yl)hexan-1-one (β-THNPH, 5). These identifications were based on liquid chromatography-quadrupole time-of-flight-mass spectrometry (LC-QTOF-MS), gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance spectroscopy (NMR). To our knowledge, no analytical data about α-PNP, 4-Cl-α-PPP, 4-Cl-α-PVP, and β-THNPH have appeared until now, making this the first report on these compounds. Moreover, in order to study the collision-induced dissociation (CID) characteristic fragmentation routes of pyrrolidinyl substituted cathinones, a total number of 13 pyrrolidinyl substituted cathinones were selected and discussed. The major fragmentation pathways under CID mode are produced, leading to the formation of characteristic ions. Product ions of [M-C4 H9 N]+ and Cn H2n N+ indicate the presence of pyrrolidinyl substitution. Characteristic fragments are also produced via the cleavages of the CH-N(CH2 )4 bond and the CO-CHN bond. Copyright © 2016 John Wiley & Sons, Ltd.

An HPLC-MS method for the quantification of new acetylcholinesterase inhibitor PC 48 (7-MEOTA-donepezil like compound) in rat plasma: Application to a pharmacokinetic study.

A simple, rapid and sensitive method based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been developed and validated for the quantitative determination in rat plasma of a new candidate for AD treatment, namely PC 48 (a 7-MEOTA-donepezil like compound) in rat plasma. Sample preparation involved pH adjustment with sodium hydroxide followed by solvent extraction with ethyl acetate:dichloromethane (80:20, v/v). The chromatographic separation was achieved on an Ascentis Express RP-Amide column (75 mm × 2.1mm, 2.7 μm) with a gradient mobile phase consisting of 0.05 M aqueous formic acid and acetonitrile. Detection was carried out using positive-ion electrospray tandem mass spectrometry on an LTQ XL system using the MS/MS CID (collision-induced dissociation) mode. The method was linear in the range 0.1-1000 ng/ml (r(2)=0.999) with a lower limit of quantitation of 0.1 ng/mL. Extraction recovery was in the range 63.5-72.1% for PC 48 and 70.5% for reserpine (internal standard, IS). Intra- and inter-day precisions measured as relative standard deviation were below 10.8% and accuracy was from -7.2% to 7.4%. The method was successfully applied to a pharmacokinetic study involving intramuscular application of 3.86 mg/kg PC 48 to rats for the first time. Pharmacokinetic parameters for PC 48 include Cmax 39.09 ± 4.45 ng/mL,Tmax 5.00 ± 3.08 min, AUC0-t 23374 ± 4045 min ng/mL and t1/2 1065 ± 246 min.

In-depth analysis of site-specific N-glycosylation in vitronectin from human plasma by tandem mass spectrometry with immunoprecipitation.

The characterization of site-specific microheterogeneity in glycoprotein is very important for understanding cell biology and disease processes. Vitronectin is well known to be a multifunctional glycoprotein in the blood and the extracellular matrix, which is related to hepatocellular carcinoma (HCC). Here, we systematically analyzed the site-specific N-glycopeptides of vitronectin in human plasma by tandem mass spectrometry combined with immunoprecipitation and hydrophilic interaction liquid chromatography (HILIC) enrichment. Vitronectin was purified with immunoprecipitation by monoclonal antibody from plasma and digested to tryptic N-glycopeptides.Then, enrichment with HILIC materials was used and followed by analysis with nano-LC/MS/MS. The sequences of N-glycopeptides were identified from the mass spectra by high-energy C-trap dissociation (HCD) and collision-induced dissociation (CID). In HCD mode, oxonium ions were used for recognizing glycopeptides and y ions for sequencing the peptide backbone. In CID mode, Y ions were used for characterizing their glycoforms. As a result, a total of 17 site-specific N-glycopeptides were completely identified in all of the three N-glycosylation sites of vitronectin in human plasma, including 12 N-glycopeptides first reported. Finally, we specifically found that three hybrid and four complex glycopeptides of triantennary forms with outer fucosylation increased in HCC human plasma.

Comparison of the activation time effects and the internal energy distributions for the CID, PQD and HCD excitation modes.

Reproducibility among different types of excitation modes is a major bottleneck in the field of tandem mass spectrometry library development in metabolomics. In this study, we specifically evaluated the influence of collision voltage and activation time parameters on tandem mass spectrometry spectra for various excitation modes [collision-induced dissociation (CID), pulsed Q dissociation (PQD) and higher-energy collision dissociation (HCD)] of Orbitrap-based instruments. For this purpose, internal energy deposition was probed using an approach based on Rice-Rampserger-Kassel-Marcus modeling with three thermometer compounds of different degree of freedom (69, 228 and 420) and a thermal model. This model treats consecutively the activation and decomposition steps, and the survival precursor ion populations are characterized by truncated Maxwell-Boltzmann internal energy distributions. This study demonstrates that the activation time has a significant impact on MS/MS spectra using the CID and PQD modes. The proposed model seems suitable to describe the multiple collision regime in the PQD and HCD modes. Linear relationships between mean internal energy and collision voltage are shown for the latter modes and the three thermometer molecules. These results suggest that a calibration based on the collision voltage should provide reproducible for PQD, HCD to be compared with CID in tandem in space instruments. However, an important signal loss is observed in PQD excitation mode whatever the mass of the studied compounds, which may affect not only parent ions but also fragment ions depending on the fragmentation parameters. A calibration approach for the CID mode based on the variation of activation time parameter is more appropriate than one based on collision voltage. In fact, the activation time parameter in CID induces a modification of the collisional regime and thus helps control the orientation of the fragmentation pathways (competitive or consecutive dissociations).

Comprehensive Cell-specific Protein Analysis in Early and Late Pollen Development from Diploid Microsporocytes to Pollen Tube Growth

Pollen development in angiosperms is one of the most important processes controlling plant reproduction and thus productivity. At the same time, pollen development is highly sensitive to environmental fluctuations, including temperature, drought, and nutrition. Therefore, pollen biology is a major focus in applied studies and breeding approaches for improving plant productivity in a globally changing climate. The most accessible developmental stages of pollen are the mature pollen and the pollen tubes, and these are thus most frequently analyzed. To reveal a complete quantitative proteome map, we additionally addressed the very early stages, analyzing eight stages of tobacco pollen development: diploid microsporocytes, meiosis, tetrads, microspores, polarized microspores, bipolar pollen, desiccated pollen, and pollen tubes. A protocol for the isolation of the early stages was established. Proteins were extracted and analyzed by means of a new gel LC-MS fractionation protocol. In total, 3817 protein groups were identified. Quantitative analysis was performed based on peptide count. Exceedingly stage-specific differential protein regulation was observed during the conversion from the sporophytic to the gametophytic proteome. A map of highly specialized functionality for the different stages could be revealed from the metabolic activity and pronounced differentiation of proteasomal and ribosomal protein complex composition up to protective mechanisms such as high levels of heat shock proteins in the very early stages of development.

Sulfur-34S Stable Isotope Labeling of Amino Acids for Quantification (SULAQ34) of Proteomic Changes in Pseudomonas fluorescens during Naphthalene Degradation

The relative quantification of proteins is one of the major techniques used to elucidate physiological reactions. Because it allows one to avoid artifacts due to chemical labeling, the metabolic introduction of heavy isotopes into proteins and peptides is the preferred method for relative quantification. For eukaryotic cells, stable isotope labeling by amino acids in cell culture (SILAC) has become the gold standard and can be readily applied in a vast number of scenarios. In the microbial realm, with its highly versatile metabolic capabilities, SILAC is often not feasible, and the use of other (13)C or (15)N labeled substrates might not be practical. Here, the incorporation of heavy sulfur isotopes is shown to be a useful alternative. We introduce (34)S stable isotope labeling of amino acids for quantification and the corresponding tools required for spectra extraction and disintegration of the isotopic overlaps caused by the small mass shift. As proof of principle, we investigated the proteomic changes related to naphthalene degradation in P. fluorescens ATCC 17483 and uncovered a specific oxidative-stress-like response.

Discrimination Between Peptide O-Sulfo- and O-Phosphotyrosine Residues by Negative Ion Mode Electrospray Tandem Mass Spectrometry

Unambiguous differentiation between isobaric sulfated and phosphorylated tyrosine residues (sTyr and pTyr) of proteins by mass spectrometry is challenging, even using high resolution mass spectrometers. Here we show that upon negative ion mode collision-induced dissociation (CID), pTyr- and sTyr-containing peptides exhibit entirely different modification-specific fragmentation patterns leading to a rapid discrimination between the isobaric covalent modifications using the tandem mass spectral data. This study reveals that the ratio between the relative abundances of [M-H-80](-) and [M-H-98](-) fragment ions in ion-trap CID and higher energy collision dissociation (HCD) spectra of singly deprotonated +80 Da Tyr-peptides can be used as a reliable indication of the Tyr modification group nature. For multiply deprotonated +80 Da Tyr-peptides, CID spectra of sTyr- and pTyr-containing sequences can be readily distinguished based on the presence/absence of the [M-nH-79]((n-1)-) and [M-nH-79-NL]((n-1)-) (n=2, 3) fragment ions (NL=neutral loss).

Tandem MS Analysis of Selenamide-Derivatized Peptide Ions

Our previous study showed that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used for selective and rapid derivatization of protein/peptide thiols in high conversion yield. This paper reports the systematic investigation of MS/MS dissociation behaviors of selenamide-derivatized peptide ions upon collision induced dissociation (CID) and electron transfer dissociation (ETD). In the positive ion mode, derivatized peptide ions exhibit tag-dependent CID dissociation pathways. For instance, ebselen-derivatized peptide ions preferentially undergo Se-S bond cleavage upon CID to produce a characteristic fragment ion, the protonated ebselen (m/z 276), which allows selective identification of thiol peptides from protein digest as well as selective detection of thiol proteins from protein mixture using precursor ion scan (PIS). In contrast, NPSP-derivatized peptide ions retain their phenylselenenyl tags during CID, which is useful in sequencing peptides and locating cysteine residues. In the negative ion CID mode, both types of tags are preferentially lost via the Se-S cleavage, analogous to the S-S bond cleavage during CID of disulfide-containing peptide anions. In consideration of the convenience in preparing selenamide-derivatized peptides and the similarity of Se-S of the tag to the S-S bond, we also examined ETD of the derivatized peptide ions to probe the mechanism for electron-based ion dissociation. Interestingly, facile cleavage of Se-S bond occurs to the peptide ions carrying either protons or alkali metal ions, while backbone cleavage to form c/z ions is severely inhibited. These results are in agreement with the Utah-Washington mechanism proposed for depicting electron-based ion dissociation processes.

Electron‐capture dissociation (ECD), collision‐induced dissociation (CID) and ECD/CID in a linear radio‐frequency‐free magnetic cell

Electron‐capture dissociation (ECD), collision‐induced dissociation (CID) and ECD/CID in a linear radio‐frequency‐free magnetic cell

Simultaneous transmission mode collision-induced dissociation and ion/ion reactions for top-down protein identification/characterization using a quadrupole/time-of-flight tandem mass spectrometer.

Simultaneous transmission mode collision-induced dissociation (CID) and ion/ion proton transfer reactions have been implemented on a quadrupole/time-of-flight (TOF) tandem mass spectrometer. Reagent anions were trapped in a pressurized quadrupole collision cell by applying appropriate dc voltages while multiply protonated protein precursor ions were injected into the collision cell at energies sufficient to give rise to CID. Intact precursor ions as well as fragment ions underwent ion/ion proton transfer reactions during their passage through the collision cell and on to an orthogonal acceleration TOF mass analyzer. The resulting product ion spectrum was then submitted to deconvolution to yield a "zero-charge" spectrum, which was then matched against in silico produced spectra derived from a protein database. Dramatic improvements in the scores associated with correct matches were obtained relative to CID data without the benefit of ion/ion reactions for proteins as large as carbonic anhydrase (29 kDa). The parameters that most affect the extent of ion/ion proton transfer during transmission through the instrument include the number of anions stored in the collision cell, the amplitude of the radio frequency trapping voltage, the voltage of the LINAC potential associated with the collision cell, and the collision gas pressure. This work demonstrates that it is possible to effect whole protein tandem mass spectrometry with simultaneous CID, ion/ion reactions, and mass analysis for high duty cycle top-down protein characterization.

High-Energy Collision Induced Dissociation of Biomolecules: MALDITOF/ RTOF Mass Spectrometry in Comparison to Tandem Sector Mass Spectrometry

MALDI in combination with high-energy collision-induced dissociation (CID) performed by tandem time-of-flight mass spectrometry (TOF/RTOF) is a relatively new technology for the structural analysis of various classes of biomolecules as e.g., peptides, carbohydrates, glycoconjugate drugs and lipids. Fragmentation mechanisms for these classes of compounds as well as corresponding fragment ion nomenclatures based mainly on data from tandem magnetic sector mass spectrometers are summarized in this article. The major instrumental differences between the present commercially available TOF/RTOFs are compiled (e.g., ion gate, gas-collision cell, type of reflectron, etc.). Whereas peptides have been investigated by MALDI-TOF/RTOF and their CID spectra are well understood, other classes of compounds (e.g., carbohydrates or lipids) are far less well investigated. By comparing data from two different MALDI-TOF/RTOF-instruments, it becomes evident that as they are operated at rather different collision energies for CID (1 versus 20 keV) strong differences in corresponding CID spectra for the same analyte are observed, causing problems with library searches in databases as e.g., abundant peptide side-chain fragmentations mainly occurring in the 8 to 20 keV collision regime are not considered. In contrast, differences in CID spectra of carbohydrates among different TOF/RTOF instruments are less clear-cut, because the required collision energy is spread across a wide range. Especially, carbohydrate cross-ring cleavages require less collision energy in the keV-range than the corresponding peptide side-chain fragmentations. Some of these carbohydrate cross-ring fragmentations are even observed by very low energy CID (< 1 eV fragmentation amplitude). Similar observations can also be made for glycoconjugates (e.g., the drug tylosin A). The lipid class triacylglycerol needs rather high collision energies for dissociating carbon-carbon bonds based upon classical charge-remote fragmentation mechanisms. Comparison of high-energy CID-data of ESI generated triacylglycerol precursors with CID spectra from MALDI generated precursors shows different mechanisms for charge-remote fragmentations. MALDI-TOF/RTOF-instruments operated in the elevated high-energy CID mode exhibit a strong potential in structural analysis of natural and synthetic biomolecules with information often not obtainable by low energy CID.

Letter: Does the Reagent Gas Influence Collisional Activation When Performing in Situ Chemical Ionization with an Ion Trap Mass Spectrometer?

Users of ion trap mass spectrometers frequently develop methods that associate chemical ionization with tandem mass spectrometry detection. With apparatus using internal ionization, the chemical reagent is present in the trap during the collision induced dissociation (CID) step and one may wonder if the reagent influences the fragmentation ratios in MS/MS. We report a comparison of the fragmentation ratios of protonated molecules when using the most common reagents (methane, ammonia, methanol, acetonitrile, isobutane) for performing in situ chemical ionization. Four molecules were chosen in the medical field to serve as models: alprazolam, diazepam, flunitrazepam and acetaminophen. In the non-resonant CID mode, the influence of the reagent mass is clearly seen in spite of its low partial pressure in the ion trap; the reagent acts as a "heavy target": the degree of fragmentation increases with the molecular weight of the reagent. In the resonant CID mode, there is no evident correlation between the fragmentation ratio of MH+ ions and the nature of the CI reagent; a slight shift of the secular frequency of the precursor ion, which tends to reduce the CID efficiency, could compensate for the "heavy target" effect underscored in the non-resonant mode.

Enrichment and Analysis of Nonenzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron-Transfer Dissociation Mass Spectrometry

Nonenzymatic glycation of peptides and proteins by d-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. However, no effective high-throughput methods exist for identifying proteins containing this low-abundance post-translational modification in bottom-up proteomic studies. In this report, phenylboronate affinity chromatography was used in a two-step enrichment scheme to selectively isolate first glycated proteins and then glycated, tryptic peptides from human serum glycated in vitro. Enriched peptides were subsequently analyzed by alternating electron-transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. ETD fragmentation mode permitted identification of a significantly higher number of glycated peptides (87.6% of all identified peptides) versus CID mode (17.0% of all identified peptides), when utilizing enrichment on first the protein and then the peptide level. This study illustrates that phenylboronate affinity chromatography coupled with LC-MS/MS and using ETD as the fragmentation mode is an efficient approach for analysis of glycated proteins and may have broad application in studies of diabetes mellitus.