Open AccessEvidence for structural variants of a- and b-type peptide fragment ions using combined ion mobility/mass spectrometry
Author(s) -
Isabel Riba-Garcia,
Kevin Giles,
Robert Bateman,
Simon J. Gaskell
Publication year - 2008
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/j.jasms.2008.01.005
Subject(s) - chemistry , fragmentation (computing) , protonation , tandem mass spectrometry , mass spectrometry , collision induced dissociation , ion mobility spectrometry , ion , dissociation (chemistry) , isobaric labeling , analytical chemistry (journal) , computational chemistry , protein mass spectrometry , chromatography , organic chemistry , computer science , operating system
Tandem mass spectrometry (MS/MS) of peptides plays a key role in the field of proteomics, and an understanding of the fragmentation mechanisms involved is vital for data interpretation. Not all the fragment ions observed by low-energy collision-induced dissociation of protonated peptides are readily explained by the generally accepted structures for a- and b-ions. The possibility of a macrocyclic structure for b-type ions has been recently proposed. In this study, we have undertaken investigations of linear protonated YAGFL-NH(2), N-acetylated-YAGFL-NH(2), and cyclo-(YAGFL) peptides and their fragments using a combination of ion mobility (IM) separation and mass spectrometry. The use of IM in this work both gives insight into relative structural forms of the ion species and crucial separation of isobaric species. Our study provides compelling evidence for the formation of a stable macrocyclic structure for the b(5) ion generated by fragmentation of protonated linear YAGFL-NH(2). Additionally we demonstrate that the a(4) ion fragment of protonated YAGFL-NH(2) has at least two structures; one of which is attributable to a macrocyclic structure on the basis of its subsequent fragmentation. More generally, this work emphasizes the value of combined IM-MS/MS in probing the detailed fragmentation mechanisms of peptide ions, and illustrates the use of combined ion mobility/collisional activation/mass spectrometry analysis in achieving an effective enhancement of the resolution of the mobility separator.