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Pseudo-MS3 in a MALDI orthogonal quadrupole-time of flight mass spectrometer
Journal article   Open access   Peer reviewed

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

Christina S Raska, Carol E Parker, Cai Huang, Jun Han, Gary L Glish, Marshall Pope and Christoph H Borchers
Journal of the American Society for Mass Spectrometry, Vol.13(9), pp.1034-1041
09/01/2002
DOI: 10.1016/S1044-0305(02)00433-6
PMID: 12322951
url
https://doi.org/10.1016/S1044-0305(02)00433-6View
Published (Version of record) Open Access

Abstract

Both the matrix selected and the laser fluence play important roles in MALDI-quadrupole/time of flight (QqTOF) fragmentation processes. "Hot" matrices, such as alpha-cyano4-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-MS3 experiments to be performed. For peptides of higher molecular weight, pseudo-MS3 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.

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