title: MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides.
abstract: In a previous report (Young et al., Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5802-5806), we provided a proof-of-principle for fold recognition of proteins using a homobifunctional amine-specific chemical crosslinking reagent in combination with mass spectrometry analysis and homology modeling. In this current work, we propose a systematic nomenclature to describe the types of peptides that are generated after proteolysis of crosslinked proteins, their fragmentation by tandem mass spectrometry, and an automated algorithm for MS/MS spectral assignment called "MS2Assign." Several examples are provided from crosslinked peptides and proteins including HIV-integrase, cytochrome c, ribonuclease A, myoglobin, cytidine 5-monophosphate N-acetylneuraminic acid synthetase, and the peptide thymopentin. Tandem mass spectra were obtained from various crosslinked peptides using post source decay MALDI-TOF and collision induced dissociation on a quadrupole-TOF instrument, along with their automated interpretation using MS2Assign. A variety of possible outcomes are described and categorized according to the number of modified lysines and/or peptide chains involved, as well as the presence of singly modified (dead-end) lysine residues. In addition, the proteolysis and chromatographic conditions necessary for optimized crosslinked peptide recovery are presented.
authors.affiliation: Buck Institute for Age Research, Novato, California 94143-0446, USA.
authors.forename: Birgit
authors.initials: B
authors.lastname: Schilling
authors.forename: Richard H
authors.initials: RH
authors.lastname: Row
authors.forename: Bradford W
authors.initials: BW
authors.lastname: Gibson
authors.forename: Xin
authors.initials: X
authors.lastname: Guo
authors.forename: Malin M
authors.initials: MM
authors.lastname: Young
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D002417:Cattle; D003432:Cross-Linking Reagents / Q000737:chemistry*; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry* / Q000145:classification; D012984:Software; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D009626:Terminology as Topic
chemical_list: D003432:Cross-Linking Reagents; D010455:Peptides