Further studies of in-source fragmentation of peptides in matrix-assisted laser desorption-ionization

Brown, Robert S.; Feng, Jun; Reiber, Duane C.

doi:10.1016/s0168-1176(97)00217-6

Cited by 66 publications

(90 citation statements)

References 31 publications

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“…This ranking is in good agreement with the increasing order of their radical-induced ISD abilities. Another characteristic of radical-induced ISD is its independence from the ionization process [30]. Indeed, Takayama et al suggest that basic amino acids near the N-terminus favor production of c-type fragments and basic amino acids near the C-terminus favor production of zand y-type fragments in positive ion mode [31,32].…”

Section: Radical-induced Pathwaymentioning

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: Radical-induced Pathwaymentioning

confidence: 99%

MALDI In-Source Decay, from Sequencing to Imaging

Debois

Smargiasso

Demeure

et al. 2012

Topics in Current Chemistry

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“…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.…”

mentioning

confidence: 99%

“…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.…”

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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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“…Zenobi and co-workers found, however, that the internal energy distributions of analyte ions did not correlate with matrix sublimation temperatures, but instead depended on gas-phase proton transfer reactions [20,21,23]. Increasing laser fluence has been shown to increase analyte ion dissociation via in-source decay (ISD) [33][34][35][36][37][38]; nevertheless, Gluckmann and Karas have questioned whether an increase in laser fluence is an accurate measure of the amount of energy transferred to the analyte [31]. Lavine and Allison [39] demonstrated that MS 3 -type experiments could be performed on a reflectron MALDI-TOF using a combination of ISD and PSD.…”

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confidence: 99%

Pseudo-MS³ in a MALDI orthogonal quadrupole-time of flight mass spectrometer

Raska

Parker

Huang

et al. 2002

J. Am. Soc. Mass Spectrom.

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Both the matrix selected and the laser fluence play important roles in MALDI-quadrupole/ time of flight (QqTOF) fragmentation processes. "Hot" matrices, such as ␣-cyano-4-hydroxycinnamic acid (HCCA), can increase fragmentation in MS spectra. Higher laser fluence also increases fragmentation. Typical peptide fragment ions observed in the QqTOF are a, b, and y ion series, which resemble low-energy CID product ions. This fragmentation may occur in the high-pressure region before the first mass-analyzing quadrupole. Fragment ions can be selected by the first quadrupole (Q1), and further sequenced by conventional MS/MS. This allows pseudo-MS 3 experiments to be performed.For peptides of higher molecular weight, pseudo-MS 3 can extend the mass range beyond what is usually accessible for sequencing, by allowing one to sequence a fragment ion of lower molecular weight instead of the full-length peptide. Peptides that predominantly show a single product ion after MS/MS yield improved sequence information when this technique is applied. This method was applied to the analysis of an in vitro phosphorylated peptide, where the intact enzymatically-generated peptide showed poor dissociation via MS/MS. Sequencing a fragment ion from the phosphopeptide enabled the phosphorylation site to be unambiguously determined. A fter the matrix-assisted laser desorption/ionization (MALDI) technique was first developed [1][2][3][4][5], there were extensive studies on the selection of matrices optimized for various types of lasers [6 -9]. Although most researchers are now primarily using 337 nm nitrogen lasers and only a few selected matrices, there has been much discussion of MALDI matrices with regard to mechanisms of ion formation [10 -24].In-source decay (ISD [25,26]) and post-source decay (PSD [27]) in MALDI/TOF-MS have been studied for the purpose of determining the mechanism of MALDI ionization, and have led to the classification of matrices such as ␣-cyano-4-hydroxycinnamic acid (HCCA) and 2,5-dihydroxybenzoic acid (DHB) as "hot" or "cold" based originally on the amount of glycoprotein fragmentation they induce [28].The differences in fragmentation observed with various matrices have been attributed to differences in initial velocities of the ions generated [29 -31], with higher initial velocities leading to cooling and less fragmentation. It has been noted that, for a given matrix, all analyte ions below 25 kDa appear to have the same initial velocity irrespective of mass, but the initial velocity depends on the matrix [31]. An early hypothesis that the internal energy and velocity of both analyte and matrix are a function of matrix sublimation temperatures has found empirical support [32]. Zenobi and co-workers found, however, that the internal energy distributions of analyte ions did not correlate with matrix sublimation temperatures, but instead depended on gas-phase proton transfer reactions [20,21,23]. Increasing laser fluence has been shown to increase analyte ion dissociation via in-source decay (ISD) [33][34][35][36][37][38...

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Further studies of in-source fragmentation of peptides in matrix-assisted laser desorption-ionization

Cited by 66 publications

References 31 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

Pseudo-MS³ in a MALDI orthogonal quadrupole-time of flight mass spectrometer

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Further studies of in-source fragmentation of peptides in matrix-assisted laser desorption-ionization

Cited by 66 publications

References 31 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

Pseudo-MS3 in a MALDI orthogonal quadrupole-time of flight mass spectrometer

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Pseudo-MS³ in a MALDI orthogonal quadrupole-time of flight mass spectrometer