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, Christoph H. Borchers

Research output: Contribution to journalArticlepeer-review

26 Citations (Scopus)


Both the matrix selected and the laser fluence play important roles in MALDI-quadrupole/time of flight (QqTOF) fragmentation processes. "Hot" matrices, such as α-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-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.

Original languageEnglish
Pages (from-to)1034-1041
Number of pages8
JournalJournal of the American Society for Mass Spectrometry
Issue number9
Publication statusPublished - Sep 2002
Externally publishedYes


Dive into the research topics of 'Pseudo-MS3 in a MALDI orthogonal quadrupole-time of flight mass spectrometer'. Together they form a unique fingerprint.

Cite this