Open AccessPseudo-MS3 in a MALDI orthogonal quadrupole-time of flight mass spectrometer
Author(s) -
Christina S. Raska,
Carol E. Parker,
Cai Huang,
Jun Han,
Gary L. Glish,
Marshall R. Pope,
Christoph H. Borchers
Publication year - 2002
Publication title -
journal of the american society for mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.961
H-Index - 127
eISSN - 1879-1123
pISSN - 1044-0305
DOI - 10.1016/s1044-0305(02)00433-6
Subject(s) - chemistry , fragmentation (computing) , mass spectrometry , ion , peptide , phosphopeptide , analytical chemistry (journal) , tandem mass spectrometry , fluence , quadrupole , mass spectrum , chromatography , atomic physics , biochemistry , organic chemistry , physics , computer science , operating system
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.