title: Development and assessment of scoring functions for protein identification using PMF data.
abstract: PMF is one of the major methods for protein identification using the MS technology. It is faster and cheaper than MS/MS. Although PMF does not differentiate trypsin-digested peptides of identical mass, which makes it less informative than MS/MS, current computational methods for PMF have the potential to improve its detection accuracy by better use of the information content in PMF spectra. We developed a number of new probability-based scoring functions for PMF protein identification based on the MOWSE algorithm. We considered a detailed distribution of matching masses in a protein database and peak intensity, as well as the likelihood of peptide matches to be close to each other in a protein sequence. Our computational methods are assessed and compared with other methods using PMF data of 52 gel spots of known protein standards. The comparison shows that our new scoring schemes have higher or comparable accuracies for protein identification in comparison to the existing methods. Our software is freely available upon request. The scoring functions can be easily incorporated into other proteomics software packages.
authors.affiliation: Computer Science Department and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO 65211-2060, USA.
authors.forename: Zhao
authors.initials: Z
authors.lastname: Song
authors.forename: Luonan
authors.initials: L
authors.lastname: Chen
authors.forename: Ashwin
authors.initials: A
authors.lastname: Ganapathy
authors.forename: Xiu-Feng
authors.initials: XF
authors.lastname: Wan
authors.forename: Laurent
authors.initials: L
authors.lastname: Brechenmacher
authors.forename: Nengbing
authors.initials: N
authors.lastname: Tao
authors.forename: David
authors.initials: D
authors.lastname: Emerich
authors.forename: Gary
authors.initials: G
authors.lastname: Stacey
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D030562:Databases, Protein; D008969:Molecular Sequence Data; D010449:Peptide Mapping / Q000379:methods; D010455:Peptides / Q000032:analysis*; D040901:Proteomics / Q000379:methods; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods
chemical_list: D010455:Peptides