Premium
Observations on the detection of b‐ and y‐type ions in the collisionally activated decomposition spectra of protonated peptides
Author(s) -
Lau King Wai,
Hart Sarah R.,
Lynch Jennifer A.,
Wong Stephen C. C.,
Hubbard Simon J.,
Gaskell Simon J.
Publication year - 2009
Publication title -
rapid communications in mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.528
H-Index - 136
eISSN - 1097-0231
pISSN - 0951-4198
DOI - 10.1002/rcm.4032
Subject(s) - chemistry , tandem mass spectrometry , ion , fragmentation (computing) , tandem , quadrupole , quadrupole ion trap , ion trap , mass spectrometry , protonation , mass spectrum , analytical chemistry (journal) , spectral line , chromatography , atomic physics , physics , organic chemistry , materials science , astronomy , computer science , composite material , operating system
Abstract Tandem mass spectrometric data from peptides are routinely used in an unsupervised manner to infer product ion sequence and hence the identity of their parent protein. However, significant variability in relative signal intensity of product ions within peptide tandem mass spectra is commonly observed. Furthermore, instrument‐specific patterns of fragmentation are observed, even where a common mechanism of ion heating is responsible for generation of the product ions. This information is currently not fully exploited within database searching strategies; this motivated the present study to examine a large dataset of tandem mass spectra derived from multiple instrumental platforms. Here, we report marked global differences in the product ion spectra of protonated tryptic peptides generated from two of the most common proteomic platforms, namely tandem quadrupole‐time‐of‐flight and quadrupole ion trap instruments. Specifically, quadrupole‐time‐of‐flight tandem mass spectra show a significant under‐representation of N‐terminal b‐type fragments in comparison to quadrupole ion trap product ion spectra. Energy‐resolved mass spectrometry experiments conducted upon test tryptic peptides clarify this disparity; b‐type ions are significantly less stable than their y‐type N‐terminal counterparts, which contain strongly basic residues. Secondary fragmentation processes which occur within the tandem quadrupole‐time‐of‐flight device account for the observed differences, whereas this secondary product ion generation does not occur to a significant extent from resonant excitation performed within the quadrupole ion trap. We suggest that incorporation of this stability information in database searching strategies has the potential to significantly improve the veracity of peptide ion identifications as made by conventional database searching strategies. Copyright © 2009 John Wiley & Sons, Ltd.