Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer:  differentiation of leucine and isoleucine

Rs, Johnson; Sa, Martin; Biemann, K.; Jt, Stults; Jt, Watson

doi:10.1021/ac00148a019

Cited by 412 publications

(306 citation statements)

References 8 publications

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“…In some cases, the very useful d-and w-type fragments are also observed [15]. These latter imply a side-chain loss whose mass depends on the amino acid residue and can therefore be useful to confirm a residue determined by two consecutive c-or z-fragments or even to distinguish the isobaric amino acid residues leucine and isoleucine [22]. Bache et al have demonstrated that ISD fragmentation occurs with a low level of hydrogen scrambling, conserving the solution deuteration pattern in the gas phase fragments formed.…”

Section: Isd Mechanismsmentioning

confidence: 99%

MALDI In-Source Decay, from Sequencing to Imaging

Debois

Smargiasso

Demeure

et al. 2012

Topics in Current Chemistry

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Matrix-assisted laser desorption/ionization (MALDI) is now a mature method allowing the identification and, more challenging, the quantification of biopolymers (proteins, nucleic acids, glycans, etc). MALDI spectra show mostly intact singly charged ions. To obtain fragments, the activation of singly charged precursors is necessary, but not efficient above 3.5 kDa, thus making MALDI MS/MS difficult for large species. In-source decay (ISD) is a prompt fragmentation reaction that can be induced thermally or by radicals. As fragments are formed in the source, precursor ions cannot be selected; however, the technique is not limited by the mass of the analyzed compounds and pseudo MS3 can be performed on intense fragments. The discovery of new matrices that enhance the ISD yield, combined with the high sensitivity of MALDI mass spectrometers, and software development, opens new perspectives. We first review the mechanisms involved in the ISD processes, then discuss ISD applications like top-down sequencing and post-translational modifications (PTMs) studies, and finally review MALDI-ISD tissue imaging applications.

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Section: Isd Mechanismsmentioning

confidence: 99%

MALDI In-Source Decay, from Sequencing to Imaging

Debois

Smargiasso

Demeure

et al. 2012

Topics in Current Chemistry

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“…The w-and d-ions are very informative fragments involving a side-chain loss, the mass of which is specific to the amino acid [42,43]. These fragments can be very helpful to confirm an amino acid deduced from two successive c-or z-ions, or for the distinction of the isobaric amino acids leucine and isoleucine.…”

Section: D- W-ions Formed From Consecutive Reaction Pathwaysmentioning

confidence: 99%

“…w-Ions are, however, not always observed even if the corresponding z-ions are observed. According to the mechanism [42,43] shown in Scheme 1, the radical fragment z • gives the w-ion by the cleavage of the C ␤ -C ␥ bond of the residue of the amino acid followed by the loss of a radical part of the residue. Therefore, not all amino acid residues can lead to that fragmentation.…”

Section: D- W-ions Formed From Consecutive Reaction Pathwaysmentioning

confidence: 99%

New advances in the understanding of the in-source decay fragmentation of peptides in MALDI-TOF-MS

Demeure

Gabelica

Pauw

2010

J. Am. Soc. Mass Spectrom.

117

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In-source decay (ISD) is a rapid fragmentation occurring in the matrix-assisted laser desorption/ionization (MALDI) source before the ion extraction. Despite the increasing interest for peptides de novo sequencing by ISD, the influence of the matrix and of the peptide itself is not yet fully understood. Here we compare matrices with high ISD efficiencies to gain deeper insight in the ISD fragmentation process(es). The major ISD fragments are the c-and z-ions, but other types of fragments are also observed, and their origin is studied here. Two main pathways lead to fragmentation in the source: a radical-induced pathway that leads to c-, z-, w-, and d-ions, and a thermally activated pathway that leads to y-, b-, and a-ions. A detailed analysis of the ISD spectra of selected peptides revealed that (1) the extents of the two in-source pathways are differently favored depending on the matrix used, that (2) the presence of a positive/negative charge on the radical-induced fragments is necessary for their observation in positive/negative mode, respectively, and that (3) [4 -9], especially peptides and proteins. In-source decay (ISD) [10,11] is a fragmentation occurring in the MALDI source, rapidly after the laser shot and before the ion extraction. ISD fragments are therefore detected at the correct m/z ratios in MS mode. On the contrary, fragments formed after the ion extraction are not resolved in MS mode, and can only be revealed by MS/MS in dual stage time-of-flight instruments [12], or by a stepwise lowering of the reflectron voltage in the so-called PSD (post source decay) mode [13,14]. ISD of peptides and proteins mainly leads to c-and z-ions [15,16], and the consensus explanation is that those fragments come from a reduction of the parent ion by hydrogen radicals coming from the matrix [17,18]. Nevertheless, other fragments such as a-, b-, and y-ions have also been reported to form in the MALDI source [4, 7-9, 19, 20]. PSD leads mainly to similar fragments as those formed by low-energy collision-induced dissociation (a-, b-, and y-ions) [21,22].Contrary to CID-like fragments, the radical-induced ISD fragments (c-and z-ions) have the advantage of being theoretically not limited in mass. Indeed, in CID experiments, the internal energy received by the peptide is distributed amongst all its degrees of freedom, i.e., they undergo intramolecular vibrational-energy redistribution (IVR). Therefore, the larger the peptide, the less the energy received per degree of freedom, decreasing the fragmentation efficiency. Like in electron capture dissociation (ECD) [23,24], because the production of c-and z-ions results from a radical-driven process that takes place before the completion of the IVR (non-ergodic process), ISD fragmentation efficiency does not depend on the mass of the peptide and allows to sequence larger peptides as well as intact proteins [5,10].In the present work, we address the mechanisms of in-source formation of the different fragment types. The difficulty in addressing these mechanisms comes from the f...

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“…Cleavage of amide bonds results in b and y ions 11,12 (see Figure 1). b ions may fragment further to produce a ions.…”

mentioning

confidence: 99%

Statistical Characterization of Ion Trap Tandem Mass Spectra from Doubly Charged Tryptic Peptides

et al. 2003

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Collision-induced dissociation (CID) is a common ion activation technique used to energize massselected peptide ions during tandem mass spectrometry. Characteristic fragment ions form from the cleavage of amide bonds within a peptide undergoing CID, allowing the inference of its amino acid sequence. The statistical characterization of these fragment ions is essential for improving peptide identification algorithms and for understanding the complex reactions taking place during CID. An examination of 1465 ion trap spectra from doubly charged tryptic peptides reveals several trends important to understanding this fragmentation process. While less abundant than y ions, b ions are present in sufficient numbers to aid sequencing algorithms. Fragment ions exhibit a characteristic series-specific relationship between their masses and intensities. Each residue influences fragmentation at adjacent amide bonds, with Pro quantifiably enhancing cleavage at its N-terminal amide bond and His increasing the formation of b ions at its C-terminal amide bond. Fragment ions corresponding to a formal loss of ammonia appear preferentially in peptides containing Gln and Asn. These trends are partially responsible for the complexity of peptide tandem mass spectra.Tandem mass spectrometry (MS/MS) of peptides is a central technology for proteomics, enabling the identification of thousands of peptides from a complex mixture. [1][2][3][4] This increasingly widespread technique relies upon the fragmentation of peptides by collisioninduced dissociation (CID), but the chemistry behind the fragmentation process is complex and not comprehensively understood. [5][6][7][8] Peptides undergo CID after they are isolated from other ions by their mass-to-charge (m/z) ratios. Peptides in an acidic solution are introduced to the vacuum of the mass spectrometer via electrospray ionization. 9 The peptide ions are accelerated during CID, leading to more energetic collisions with the ion trap's inert gas molecules. The mobile proton model 10 describes how the added internal energy causes the ionizing proton(s) on each peptide to transfer intramolecularly until one destabilizes a peptide bond, resulting in the cleavage of that bond and the production of two fragments. While more energetic techniques may cleave many classes of bonds within the peptide structure, low-energy CID preferentially breaks the amide bonds. Once the fragment ions are produced, the mass spectrometer records their m/z ratios in a tandem mass spectrum.Determining the sequence of a peptide from its tandem spectrum is complicated by the variety and variability of the fragment ions produced. Cleavage of amide bonds results in b and y Figure 1). b ions may fragment further to produce a ions. 13 If only these three ions were produced for every amide bond in a 10-residue peptide, the fragment ion spectrum would contain 27 peaks. This ideal spectrum differs from experimental spectra as a result of several causes. First, a subset of the expected fragment ions may not be present. Second...

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Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: differentiation of leucine and isoleucine

Cited by 412 publications

References 8 publications

MALDI In-Source Decay, from Sequencing to Imaging

MALDI In-Source Decay, from Sequencing to Imaging

New advances in the understanding of the in-source decay fragmentation of peptides in MALDI-TOF-MS

Statistical Characterization of Ion Trap Tandem Mass Spectra from Doubly Charged Tryptic Peptides

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