title: The fate of b-ions in the two worlds of collision-induced dissociation.
abstract: Fragment analysis of proteins and peptides by mass spectrometry using collision-induced dissociation (CID) revealed that the pairwise generated N-terminal b- and C-terminal y-ions have different stabilities resulting in underrepresentation of b-ions. Detailed analyses of large-scale spectra databases and synthetic peptides underlined these observations and additionally showed that the fragmentation pattern depends on utilized CID regime. To investigate this underrepresentation further we systematically compared resonant excitation energy and beam-type CID facilitated on different mass spectrometer platforms: (i) quadrupole time-of-flight, (ii) linear ion trap and (iii) three-dimensional ion trap. Detailed analysis of MS/MS data from a standard tryptic protein digest revealed that b-ions are significantly underrepresented on all investigated mass spectrometers. By N-terminal acetylation of tryptic peptides we show for the first time that b-ion cyclization reaction significantly contributes to b-ion underrepresentation even on ion trap instruments and accounts for at most 16% of b-ion loss.
authors.affiliation: Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum (BMFZ), Heinrich-Heine-Universität, Düsseldorf, Germany. Electronic address: daniel.waldera-lupa@uni-duesseldorf.de.
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Waldera-Lupa
authors.forename: Anja
authors.initials: A
authors.lastname: Stefanski
authors.forename: Helmut E
authors.initials: HE
authors.lastname: Meyer
authors.forename: Kai
authors.initials: K
authors.lastname: Stühler
mesh_terms: D000818:Animals; D001234:Aspergillus niger / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry; D019117:Burkholderia / Q000201:enzymology; D002417:Cattle; D030562:Databases, Protein; D005656:Fungal Proteins / Q000737:chemistry; D005949:Glucose Oxidase / Q000737:chemistry; D008049:Lipase / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D038201:alpha-Crystallins / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D005656:Fungal Proteins; D010455:Peptides; D038201:alpha-Crystallins; D005949:Glucose Oxidase; D008049:Lipase
keywords: Ac; Collision-induced dissociation; ETD; HCD; HSD; LIT; Mass spectrometry; Peptide acetylation; Peptide fragmentation; QIT; QQQ; QToF; UPLC; acetylated; b-Ion cyclization; electron transfer dissociation; higher-energy collisional dissociation; honestly significant difference; linear ion trap; nAc; non-acetylated; quadrupole ion trap; quadrupole time-of-flight; triple quadrupole; ultra performance liquid chromatography