title: A programmable fragmentation analysis of proteins by in-source decay in MALDI-TOF mass spectrometry.
abstract: Here we describe an algorithm for identifying peptides/ proteins of known sequence and unknown peptides from partial spectra generated by an in-source decay (ISD) technique coupled with matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry. The identification of protein fragments is processed with a software program called CMATCH, which generates candidate subsequences for both known peptides/proteins and unknown peptides for the major product ions in the spectral range m/z 400-5000 and then matches these to known protein sequences contained in a reference database for the known peptides/proteins. CMATCH, which is compiled for MSDOS or WINDOWS95/NT, has two main advantages: first, the candidate subsequences are generated automatically without the need for supplementary information concerning the distribution of either N-terminal or C-terminal ions in the spectra for both known peptides/proteins and unknown peptides; second, the highest coordinated homologous sequences are picked up automatically from the reference database as the best matches with known peptides/proteins. Examples from the ISD spectra of several test proteins demonstrate the efficacy of this protein identification software.
authors.affiliation: Proteomics Laboratory, Amakubo, Tsukuba, Japan. jl_g@hotmail.com
authors.forename: Jialing
authors.initials: J
authors.lastname: Gao
authors.forename: Akira
authors.initials: A
authors.lastname: Tsugita
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Takayama
authors.forename: Lin
authors.initials: L
authors.lastname: Xu
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D002138:Calibration; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
chemical_list: D011506:Proteins