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1.
The dissociation of intermolecularly crosslinked peptides was evaluated for a series of peptides with proline or aspartic acid residues positioned adjacent to the crosslinking sites (lysine residues). The peptides were crosslinked with either disuccinimidyl suberate (DSS) or disuccinimidyl L-tartrate (DST), and the influence of proline and aspartic acid residues on the fragmentation patterns were investigated for precursor ions with and without a mobile proton. Collisionally activated dissociation (CAD) spectra of aspartic acid-containing crosslinked peptide ions, doubly-charged with both protons sequestered, were dominated by cleavage C-terminal to the Asp residue, similar to that of unmodified peptides. The proline-containing crosslinked peptides exhibited a high degree of internal ion formation, with the resulting product ions having an N-terminal proline residue. Upon dissociation of the doubly-charged crosslinked peptides, twenty to fifty percent of the fragment ion abundance was accounted for by multiple cleavage products. Crosslinked peptides possessing a mobile proton yielded almost a full series of b- and y-type fragment ions, with only proline-directed fragments still observed at high abundances. Interestingly, the crosslinked peptides exhibited a tendency to dissociate at the amide bond C-terminal to the crosslinked lysine residue, relative to the N-terminal side. One could envision updating computer algorithms to include these crosslinker specific product ions--particularly for precursor ions with localized protons--that provide complementary and confirmatory information, to offer more confident identification of both the crosslinked peptides and the location of the crosslink, as well as affording predictive guidelines for interpretation of the product-ion spectra of crosslinked peptides. 相似文献
2.
Influence of crosslinker identity and position on gas-phase dissociation of lys-lys crosslinked peptides 总被引:1,自引:0,他引:1
Gaucher SP Hadi MZ Young MM 《Journal of the American Society for Mass Spectrometry》2006,17(3):395-405
A systematic study of the dissociation patterns of crosslinked peptides analyzed by tandem mass spectrometry is reported. A series of 11-mer peptides was designed around either a polyalanine or polyglycine scaffold with arginine at the C terminus. One or two lysine residues were included at various locations within the peptides to effect inter- or intra-molecular crosslinking, respectively. Crosslinked species were generated with four commonly used amine-specific chemical crosslinking reagents: disuccinimidyl suberate (DSS), disuccinimidyl tartarate (DST), dithiobis(succinimidylpropionate) (DSP), and disuccinimidyl glutarate (DSG). The influence of precursor charge state, location of crosslink, and specific crosslinking reagent on the MS/MS dissociation pattern was examined. Observed trends in the dissociation patterns obtained for these species will allow for improvements to software used in the automated interpretation of crosslinked peptide MS/MS data. 相似文献
3.
Peter Max Gehrig Bernd Roschitzki Dorothea Rutishauser Sonja Reiland Ralph Schlapbach 《Rapid communications in mass spectrometry : RCM》2009,23(10):1435-1445
In order to investigate gas‐phase fragmentation reactions of phosphorylated peptide ions, matrix‐assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) tandem mass (MS/MS) spectra were recorded from synthetic phosphopeptides and from phosphopeptides isolated from natural sources. MALDI‐TOF/TOF (TOF: time‐of‐flight) spectra of synthetic arginine‐containing phosphopeptides revealed a significant increase of y ions resulting from bond cleavages on the C‐terminal side of phosphothreonine or phosphoserine. The same effect was found in ESI‐MS/MS spectra recorded from the singly charged but not from the doubly charged ions of these phosphopeptides. ESI‐MS/MS spectra of doubly charged phosphopeptides containing two arginine residues support the following general fragmentation rule: Increased amide bond cleavage on the C‐terminal side of phosphorylated serines or threonines mainly occurs in peptide ions which do not contain mobile protons. In MALDI‐TOF/TOF spectra of phosphopeptides displaying N‐terminal fragment ions, abundant b–H3PO4 ions resulting from the enhanced dissociation of the pSer/pThr–X bond were detected (X denotes amino acids). Cleavages at phosphoamino acids were found to be particularly predominant in spectra of phosphopeptides containing pSer/pThr–Pro bonds. A quantitative evaluation of a larger set of MALDI‐TOF/TOF spectra recorded from phosphopeptides indicated that phosphoserine residues in arginine‐containing peptides increase the signal intensities of the respective y ions by almost a factor of 3. A less pronounced cleavage‐enhancing effect was observed in some lysine‐containing phosphopeptides without arginine. The proposed peptide fragmentation pathways involve a nucleophilic attack by phosphate oxygen on the carbon center of the peptide backbone amide, which eventually leads to cleavage of the amide bond. Copyright © 2009 John Wiley & Sons, Ltd. 相似文献
4.
Various peptide modifications have been explored recently to facilitate the acquisition of sequence information. N-terminal sulfonation is an interesting modification because it allows unambiguous de novo sequencing of peptides, especially in conjunction with MALDI-PSD-TOF analysis; such modified peptide ions undergo fragmentation at energies lower than those required conventionally for unmodified peptide ions. In this study, we systematically investigated the fragmentation mechanisms of N-terminal sulfonated peptide ions prepared using two different N-terminal sulfonation reagents: 4-sulfophenyl isothiocyanate (SPITC) and 4-chlorosulfophenyl isocyanate (SPC). Collision-induced dissociation (CID) of the SPC-modified peptide ions produced a set of y-series ions that were more evenly distributed relative to those observed for the SPITC-modified peptides; y(n-1) ion peaks were consistently and significantly larger than the signals of the other y-ions. We experimentally investigated the differences between the dissociation energies of the SPITC- and SPC-modified peptide ions by comparing the MS/MS spectra of the complexes formed between the crown ether 18-crown-6 (CE) and the modified peptides. Upon CID, the complexes formed between 18-crown-6 ether and the protonated amino groups of C-terminal lysine residues underwent either peptide backbone fragmentation or complex dissociation. Although the crown ether complexes of the unmodified ([M + CE + 2H]2+) and SPC-modified ([M* + CE + 2H]2+) peptides underwent predominantly noncovalent complex dissociation upon CID, the low-energy dissociations of the crown ether complexes of the SPITC-modified peptides ([M' + CE + 2H]2+) unexpectedly resulted in peptide backbone fragmentations, along with a degree of complex dissociation. We performed quantum mechanical calculations to address the energetics of fragmentations observed for the modified peptides. 相似文献
5.
Schilling B Row RH Gibson BW Guo X Young MM 《Journal of the American Society for Mass Spectrometry》2003,14(8):834-850
In a previous report (Young et al., Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5802-5806), we provided a proof-of-principle for fold recognition of proteins using a homobifunctional amine-specific chemical crosslinking reagent in combination with mass spectrometry analysis and homology modeling. In this current work, we propose a systematic nomenclature to describe the types of peptides that are generated after proteolysis of crosslinked proteins, their fragmentation by tandem mass spectrometry, and an automated algorithm for MS/MS spectral assignment called "MS2Assign." Several examples are provided from crosslinked peptides and proteins including HIV-integrase, cytochrome c, ribonuclease A, myoglobin, cytidine 5-monophosphate N-acetylneuraminic acid synthetase, and the peptide thymopentin. Tandem mass spectra were obtained from various crosslinked peptides using post source decay MALDI-TOF and collision induced dissociation on a quadrupole-TOF instrument, along with their automated interpretation using MS2Assign. A variety of possible outcomes are described and categorized according to the number of modified lysines and/or peptide chains involved, as well as the presence of singly modified (dead-end) lysine residues. In addition, the proteolysis and chromatographic conditions necessary for optimized crosslinked peptide recovery are presented. 相似文献
6.
Soderblom EJ Bobay BG Cavanagh J Goshe MB 《Rapid communications in mass spectrometry : RCM》2007,21(21):3395-3408
Chemical crosslinking combined with mass spectrometry is a useful tool for studying the topological organization of multiprotein interactions, but it is technically challenging to identify peptides involved in a crosslink using tandem mass spectrometry (MS/MS) due to the presence of product ions originating from both peptides within the same crosslink. We have previously developed a novel set of collision-induced dissociative chemical crosslinking reagents (CID-CXL reagents) that incorporate a labile bond within the linker which readily dissociates at a single site under low-energy collision-induced dissociation (CID) to enable independent isolation and sequencing of the crosslinked peptides by traditional MS/MS and database searching. Alternative low-energy CID events were developed within the in-source region by increasing the multipole DC offset voltage (ISCID) or within the ion trap by increasing the collisional excitation (ITCID). Both dissociation events, each having their unique advantages, occur without significant backbone fragmentation to the peptides, thus permitting subsequent CID to be applied to these distinct peptide ions for generation of suitable product ion spectra for database searching. Each approach was developed and applied to a chemical crosslinking study involving the N-terminal DNA-binding domain of AbrB (AbrBN), a transition-state regulator in Bacillus subtilis. A total of thirteen unique crosslinks were identified using the ITCID approach which represented a significant improvement over the eight unique crosslinks identified using the ISCID approach. The ability to segregate intrapeptide and interpeptide crosslinks using ITCID represents the first step towards high-throughput analysis of protein-protein crosslinks using our CID-CXL reagents. 相似文献
7.
Eric S. Simon Panagiotis G. Papoulias Philip C. Andrews 《Journal of the American Society for Mass Spectrometry》2010,21(9):1624-1632
The fragmentation characteristics of peptides derivatized at the side-chain ε-amino group of lysyl residues via reductive
amination with benzaldehyde have been examined using collision-induced dissociation (CID) tandem mass spectrometry. The resulting
MS/MS spectra exhibit peaks representing product ions formed from two independent fragmentation pathways. One pathway results
in backbone fragmentation and commonly observed sequence ion peaks. The other pathway corresponds to the unsymmetrical, heterolytic
cleavage of the Cζ-Nε bond that links the benzyl derivative to the side-chain lysyl residue. This results in the elimination of the derivative
as a benzylic or tropylium carbocation and a (n − l)+-charged peptide product (where n is the precursor ion charge state). The frequency of occurrence of the elimination pathway
increases with increasing charge of the precursor ion. For the benzylmodified tryptic peptides analyzed in this study, peaks
representing products from both of these pathways are observed in the MS/MS spectra of doubly-charged precursor ions, but
the carbocation elimination pathway occurs almost exclusively for triply-charged precursor ions. The experimental evidence
presented herein, combined with molecular orbital calculations, suggests that the elimination pathway is a charge-directed
reaction contingent upon protonation of the secondary ε-amino group of the benzyl-derivatized lysyl side chain. If the secondary
ε-amine is protonated, the elimination of the carbocation is observed. If the precursor is not protonated at the secondary
ε-amine, backbone fragmentation persists. The application of appropriately substituted benzyl analogs may allow for selective
control over the relative abundance of product ions generated from the two pathways. 相似文献
8.
Clifford-Nunn B Showalter HD Andrews PC 《Journal of the American Society for Mass Spectrometry》2012,23(2):201-212
Mapping protein interactions and their dynamics is crucial to defining physiologic states, building effective models for understanding
cell function, and to allow more effective targeting of new drugs. Crosslinking studies can estimate the proximity of proteins,
determine sites of protein–protein interactions, and have the potential to provide a snapshot of dynamic interactions by covalently
locking them in place for analysis. Several major challenges are associated with the use of crosslinkers in mass spectrometry,
particularly in complex mixtures. We describe the synthesis and characterization of a MS-cleavable crosslinker containing
cyclic amines, which address some of these challenges. The DC4 crosslinker contains two intrinsic positive charges, which
allow crosslinked peptides to fragment into their component peptides by collision-induced dissociation (CID) or in-source
decay. Initial fragmentation events result in cleavage on either side of the positive charges so crosslinked peptides are
identified as pairs of ions separated by defined masses. The structures of the component peptides can then be robustly determined
by MS3 because their fragmentation products rearrange to generate a mobile proton. The DC4 crosslinking reagent is stable to storage,
highly reactive, highly soluble (1 M solutions), quite labile to CID, and MS3 results in productive backbone fragmentation. 相似文献
9.
Leixiaomeng Fu Tingting Chen Gaiqing Xue Lily Zu Weihai Fang 《Journal of mass spectrometry : JMS》2013,48(1):128-134
Selective cleavage is of great interest in mass spectrometry studies as it can help sequence identification by promoting simple fragmentation pattern of peptides and proteins. In this work, the collision‐induced dissociation of peptides containing internal lysine and acetylated lysine residues were studied. The experimental and computational results revealed that multiple fragmentation pathways coexisted when the lysine residue was two amino acid residues away from N‐terminal of the peptide. After acetylation of the lysine side‐chain, ions were the most abundant primary fragment products and the Lys(Ac)–Gly amide bond became the dominant cleavage site via an oxazolone pathway. Acetylating the side‐chain of lysine promoted the selective cleavage of Lys–Xxx amide bond and generated much more information of the peptide backbone sequence. The results re‐evaluate the selective cleavage due to the lysine basic side‐chain and provide information for studying the post‐translational modification of proteins and other bio‐molecules containing Lys residues. Copyright © 2013 John Wiley & Sons, Ltd. 相似文献
10.
Back JW Hartog AF Dekker HL Muijsers AO de Koning LJ de Jong L 《Journal of the American Society for Mass Spectrometry》2001,12(2):222-227
Mass spectrometric structural analysis of crosslinked peptides is a powerful method to elucidate the spatial arrangement of polypeptides in protein complexes. Our aim is to develop bifunctional crosslinkers that, after crosslinking protein complexes followed by proteolytic digestion, give rise to crosslinked peptides that can be readily tracked down by mass spectrometry. To this end we synthesized the crosslinker N-benzyliminodiacetoyloxysuccinimid (BID), which yields stable benzyl cation marker ions upon low-energy collision-induced dissociation (CID) tandem mass spectrometry. Sensitive detection of the marker ion upon low-energy CID is demonstrated with different BID-crosslinked peptide preparations. With BID it becomes possible to retrieve crosslinked and crosslinker-adducted peptides, without the necessity of purifying crosslinked peptides prior to identification. The basic design of this crosslinker can be varied upon, in order to meet specific crosslinking needs. 相似文献
11.
Shibdas Banerjee Shyamalava Mazumdar 《Journal of the American Society for Mass Spectrometry》2012,23(11):1967-1980
The gas-phase peptide ion fragmentation chemistry is always the center of attraction in proteomics to analyze the amino acid sequence of peptides and proteins. In this work, we describe the formation of an anomalous fragment ion, which corresponds to the selective deletion of the internal lysine residue from a series of lysine containing peptides upon collisional activation in the ion trap. We detected several water-loss fragment ions and the maximum number of water molecules lost from a particular fragment ion was equal to the number of lysine residues in that fragment. As a consequence of this water-loss phenomenon, internal lysine residues were found to be deleted from the peptide ion. The N,N-dimethylation of all the amine functional groups of the peptide stopped the internal lysine deletion reaction, but selective N-terminal ??-amino acetylation had no effect on this process indicating involvement of the side chains of the lysine residues. The detailed mechanism of the lysine deletion was investigated by multistage CID of the modified and unmodified peptides, by isotope labeling and by energy resolved CID studies. The results suggest that the lysine deletion might occur through a unimolecular multistep mechanism involving a seven-membered cyclic imine intermediate formed by the loss of water from a lysine residue in the protonated peptide. This intermediate subsequently undergoes degradation reaction to deplete the interior imine ring from the peptide backbone leading to the deletion of an internal lysine residue. 相似文献
12.
Cole SR Ma X Zhang X Xia Y 《Journal of the American Society for Mass Spectrometry》2012,23(2):310-320
The fragmentation chemistry of peptides containing intrachain disulfide bonds was investigated under electron transfer dissociation
(ETD) conditions. Fragments within the cyclic region of the peptide backbone due to intrachain disulfide bond formation were
observed, including: c (odd electron), z (even electron), c-33 Da, z + 33 Da, c + 32 Da, and z–32 Da types of ions. The presence
of these ions indicated cleavages both at the disulfide bond and the N–Cα backbone from a single electron transfer event.
Mechanistic studies supported a mechanism whereby the N–Cα bond was cleaved first, and radical-driven reactions caused cleavage
at either an S–S bond or an S–C bond within cysteinyl residues. Direct ETD at the disulfide linkage was also observed, correlating
with signature loss of 33 Da (SH) from the charge-reduced peptide ions. Initial ETD cleavage at the disulfide bond was found
to be promoted amongst peptides ions of lower charge states, while backbone fragmentation was more abundant for higher charge
states. The capability of inducing both backbone and disulfide bond cleavages from ETD could be particularly useful for sequencing
peptides containing intact intrachain disulfide bonds. ETD of the 13 peptides studied herein all showed substantial sequence
coverage, accounting for 75%–100% of possible backbone fragmentation. 相似文献
13.
Wang J Zhang J Arbogast B Maier CS 《Journal of the American Society for Mass Spectrometry》2011,22(10):1771-1783
Fixed charge chemical modifications on peptides and proteins can impact fragmentation behaviors in tandem mass spectrometry
(MS/MS). In this study, we employed a thiol-specific cationic alkylation reagent, (4-iodobutyl)triphenylphosphonium (IBTP),
to selectively modify cysteine thiol groups in mitochondrial proteome samples. Tandem mass spectrometric characteristics of
butyltriphenylphosphonium (BTP)-modified peptides were evaluated by comparison to their carbamidomethylated (CAM) analogues
using a quadrupole time-of-flight (Q-TOF) instrument under low energy collision-induced dissociation (CID) conditions. Introduction
of the fixed charge modification resulted in the observation of peptide and fragment (bn and yn) ions with higher charge states than those observed for CAM-modified analogues. The charged BTP moiety had a significant
effect on the neighboring amide bond fragmentation products. A decrease in relative abundances of the product ions at the
corresponding cleavage sites was observed compared with those from the CAM-modified derivatives. This effect was particularly
noticeable when an Xxx-Pro bond was in the vicinity of a BTP group. We hypothesized that the presence of a phosphonium moiety
will reduce the tendency for protonation of the proximal amide bonds in the peptide backbone. Indeed, calculations indicated
that proton affinities of backbone amide bonds close to the modified cysteine residues were generally 20–50 kcal/mol lower
for BTP-modified peptides than for the unmodified or CAM-modified analogues with the sequence motif -Ala-Cys-Alan-Ala2-, -Ala-Cys-Alan-Pro-Ala-, and -Ala-Pro-Alan-Cys-Ala-, n = 0–3. 相似文献
14.
Zhang Y Zhang H Cui W Chen H 《Journal of the American Society for Mass Spectrometry》2011,22(9):1610-1621
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. 相似文献
15.
Andrew W. Jones Peter J. Winn Helen J. Cooper 《Journal of the American Society for Mass Spectrometry》2012,23(12):2063-2074
The radical ion chemistry of a suite of S-nitrosopeptides has been investigated. Doubly and triply-protonated ions of peptides NYCGLPGEYWLGNDK, NYCGLPGEYWLGNDR, NYCGLPGERWLGNDR, NACGAPGEKWAGNDK, NYCGLPGEKYLGNDK, NYGLPGCEKWYGNDK and NYGLPGEKWYGCNDK were subjected to electron capture dissociation (ECD), and collision-induced dissociation (CID). The peptide sequences were selected such that the effect of the site of S-nitrosylation, the nature and position of the basic amino acid residues, and the nature of the other amino acid side chains, could be interrogated. The ECD mass spectra were dominated by a peak corresponding to loss of ?NO from the charge-reduced precursor, which can be explained by a modified Utah-Washington mechanism. Some backbone fragmentation in which the nitrosyl modification was preserved was also observed in the ECD of some peptides. Molecular dynamics simulations of peptide ion structure suggest that the ECD behavior was dependent on the surface accessibility of the protonated residue. CID of the S-nitrosylated peptides resulted in homolysis of the S?CN bond to form a long-lived radical with loss of ?NO. The radical peptide ions were isolated and subjected to ECD and CID. ECD of the radical peptide ions provided an interesting comparison to ECD of the unmodified peptides. The dominant process was electron capture without further dissociation (ECnoD). CID of the radical peptide ions resulted in cysteine, leucine, and asparagine side chain losses, and radical-induced backbone fragmentation at tryptophan, tyrosine, and asparagine residues, in addition to charge-directed backbone fragmentation. 相似文献
16.
Bhaskar Godugu Pedatsur Neta Yamil Simón-Manso Stephen E. Stein 《Journal of the American Society for Mass Spectrometry》2010,21(7):1169-1176
A prominent dissociation path for electrospray generated tryptic peptide ions is the dissociation of the peptide bond linking
the second and third residues from the ammo-terminus. The formation of the resulting b2 and y
n−2 fragments has been rationalized by specific facile mechanisms. An examination of spectral libraries shows that this path
predominates in diprotonated peptides composed of 12 or fewer residues, with the notable exception of peptides containing
glutamine or glutamic acid at the N-terminus. To elucidate the mechanism by which these amino acids affect peptide fragmentation,
we synthesized peptides of varying size and composition and examined their MS/MS spectra as a function of collision voltage
in a triple quadrupole mass spectrometer. Loss of water from N-terminal glutamic acid and glutamine is observed at a lower
voltage than any other fragmentation, leading to cyclization of the terminal residue. This cyclization results in the conversion
of the terminal amine group to an imide, which has a lower proton affinity. As a result, the second proton is not localized
at the N-terminus but is readily transferred to other sites, leading to fragmentation near the center of the peptide. Further
confirmation was obtained by examining peptides with N-terminal pyroglutamic acid and N-acetyl peptides. Peptides with N-terminal
proline maintain the trend of forming b2 and y
n−2 because their ring contains an imine rather than imide and has sufficient proton affinity to retain the proton at the N-terminus. 相似文献
17.
Yin H Chacon A Porter NA Masterson DS 《Journal of the American Society for Mass Spectrometry》2007,18(5):807-816
Protein identification is routinely accomplished by peptide sequencing using mass spectrometry (MS) after enzymatic digestion.
Site-specific chemical modification may improve peptide ionization efficiency or sequence coverage in mass spectrometry. We
report herein that amino group of lysine residue in peptides can be selectively modified by reaction with a peroxycarbonate
and the resulting lysine peroxycarbamates undergo homolytic fragmentation under conditions of low-energy collision-induced
dissociation (CID) in electrospray ionization (ESI) and matrix-assisted laser desorption and ionization (MALDI) MS. Selective
modification of lysine residue in peptides by our strategy can induce specific peptide cleavage at or near the lysine site.
Studies using deuterated analogues of modified lysine indicate that fragmentation of the modified peptides involves apparent
free-radical processes that lead to peptide chain fragmentation and side-chain loss. The formation of a-, c-, or z-types of
ions in MS is reminiscent of the proposed free-radical mechanisms in low-energy electron capture dissociation (ECD) processes
that may have better sequence coverage than that of the conventional CID method. This site-specific cleavage of peptides by
free radical- promoted processes is feasible and such strategies may aid the protein sequencing analysis and have potential
applications in top-down proteomics. 相似文献
18.
Dupré M Cantel S Martinez J Enjalbal C 《Journal of the American Society for Mass Spectrometry》2012,23(2):330-346
By screening a data set of 392 synthetic peptides MS/MS spectra, we found that a known C-terminal rearrangement was unexpectedly
frequently occurring from monoprotonated molecular ions in both ESI and MALDI tandem mass spectrometry upon low and high energy
collision activated dissociations with QqTOF and TOF/TOF mass analyzer configuration, respectively. Any residue localized
at the C-terminal carboxylic acid end, even a basic one, was lost, provided that a basic amino acid such arginine and to a
lesser extent histidine and lysine was present in the sequence leading to a fragment ion, usually depicted as (bn-1 + H2O) ion, corresponding to a shortened non-scrambled peptide chain. Far from being an epiphenomenon, such a residue exclusion
from the peptide chain C-terminal extremity gave a fragment ion that was the base peak of the MS/MS spectrum in certain cases.
Within the frame of the mobile proton model, the ionizing proton being sequestered onto the basic amino acid side chain, it
is known that the charge directed fragmentation mechanism involved the C-terminal carboxylic acid function forming an anhydride
intermediate structure. The same mechanism was also demonstrated from cationized peptides. To confirm such assessment, we
have prepared some of the peptides that displayed such C-terminal residue exclusion as a C-terminal backbone amide. As expected
in this peptide amide series, the production of truncated chains was completely suppressed. Besides, multiply charged molecular
ions of all peptides recorded in ESI mass spectrometry did not undergo such fragmentation validating that any mobile ionizing
proton will prevent such a competitive C-terminal backbone rearrangement. Among all well-known nondirect sequence fragment
ions issued from non specific loss of neutral molecules (mainly H2O and NH3) and multiple backbone amide ruptures (b-type internal ions), the described C-terminal residue exclusion is highly identifiable
giving raise to a single fragment ion in the high mass range of the MS/MS spectra. The mass difference between this signal
and the protonated molecular ion corresponds to the mass of the C-terminal residue. It allowed a straightforward identification
of the amino acid positioned at this extremity. It must be emphasized that a neutral residue loss can be misattributed to
the formation of a ym-1 ion, i.e., to the loss of the N-terminal residue following the a1-ym–1 fragmentation channel. Extreme caution must be adopted when reading the direct sequence ion on the positive ion MS/MS spectra
of singly charged peptides not to mix up the attribution of the N- and C-terminal amino acids. Although such peculiar fragmentation
behavior is of obvious interest for de novo peptide sequencing, it can also be exploited in proteomics, especially for studies
involving digestion protocols carried out with proteolytic enzymes other than trypsin (Lys-N, Glu-C, and Asp-N) that produce
arginine-containing peptides. 相似文献
19.
Presented is a method for analyzing sulfated peptides, and differentiating the post-translational modification (PTM) from its isobaric counterpart phosphorylation, using quadrupole time-of-flight (Qq/TOF) mass spectrometry (MS) and positive ion nanoelectrospray MS/MS. A set of commercially available sulfo- and phosphopeptide standards was analyzed via in-source dissociation and MS/MS to generate fragmentation signatures that were used to characterize and differentiate the two modifications. All of the phosphorylated peptides retained their +80 Da modifications under collision-induced decomposition (CID) conditions and peptide backbone fragmentation allowed for the site-specific identification of the modification. In sharp contrast, sulfated peptides lost SO3 from the precursor as the collision energy (CE) was increased until only the non-sulfated form of the peptide was observed. The number of 80 Da losses indicated the number of sulfated sites. By continuing to ramp the CE further, it was possible to fragment the non-sulfated peptides and obtain detailed sequence information. It was not possible to obtain site-specific information on the location of the sulfate moieties using positive ion MS/MS as none of the original precursor ions were present at the time of peptide backbone fragmentation. This method was applied to the analysis of recombinant human B-domain deleted factor VIII (BDDrFVIII), which has six well-documented sulfation sites and several potential phosphorylation sites located in two of the sulfated regions of the protein. Seven peptides with single and multiple +80 Da modifications were isolated and analyzed for their respective PTMs. The fragmentation patterns obtained from the BDDrFVIII peptides were compared with those obtained for the standard peptides; and in all cases the peptides were sulfated. None of the potential phosphorylation sites were found to be occupied, and these results are consistent with the literature. 相似文献
20.
Chalkley RJ Brinkworth CS Burlingame AL 《Journal of the American Society for Mass Spectrometry》2006,17(9):1271-1274
The recent development of novel fragmentation processes based on either electron capture directly or transfer from an anion show great potential for solving problems in proteomics that are intractable by the more widely employed thermal-based fragmentation processes such as collision induced dissociation. The dominant fragmentation occurring upon electron capture dissociation of peptides is cleavage of N-C alpha bonds in the peptide backbone to form c and z* ions. In the case of disulfide-linked peptides, it has also been shown that electron capture on one of the cystine sulfur atoms is favored, resulting in cleavage of the disulfide bond. In this study, we report that electron capture on the sulfur of alkylated cysteine residues is also a dominant process, causing cysteine side-chain loss from z* ions. 相似文献