title: Fast and accurate identification of semi-tryptic peptides in shotgun proteomics.
abstract: BACKGROUND
  One of the major problems in shotgun proteomics is the low peptide coverage when analyzing complex protein samples. Identifying more peptides, e.g. non-tryptic peptides, may increase the peptide coverage and improve protein identification and/or quantification that are based on the peptide identification results. Searching for all potential non-tryptic peptides is, however, time consuming for shotgun proteomics data from complex samples, and poses a challenge for a routine data analysis.
  
  
  RESULTS
  We hypothesize that non-tryptic peptides are mainly created from the truncation of regular tryptic peptides before separation. We introduce the notion of truncatability of a tryptic peptide, i.e. the probability of the peptide to be identified in its truncated form, and build a predictor to estimate a peptide's truncatability from its sequence. We show that our predictions achieve useful accuracy, with the area under the ROC curve from 76% to 87%, and can be used to filter the sequence database for identifying truncated peptides. After filtering, only a limited number of tryptic peptides with the highest truncatability are retained for non-tryptic peptide searching. By applying this method to identification of semi-tryptic peptides, we show that a significant number of such peptides can be identified within a searching time comparable to that of tryptic peptide identification.
authors.affiliation: School of Informatics, Bloomington, IN, USA.
authors.forename: Pedro
authors.initials: P
authors.lastname: Alves
authors.forename: Randy J
authors.initials: RJ
authors.lastname: Arnold
authors.forename: David E
authors.initials: DE
authors.lastname: Clemmer
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
authors.forename: James P
authors.initials: JP
authors.lastname: Reilly
authors.forename: Quanhu
authors.initials: Q
authors.lastname: Sheng
authors.forename: Haixu
authors.initials: H
authors.lastname: Tang
authors.forename: Zhiyin
authors.initials: Z
authors.lastname: Xun
authors.forename: Rong
authors.initials: R
authors.lastname: Zeng
authors.forename: Predrag
authors.initials: P
authors.lastname: Radivojac
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D008969:Molecular Sequence Data; D010449:Peptide Mapping / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D020543:Proteome / Q000737:chemistry*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D014357:Trypsin / Q000737:chemistry*
chemical_list: D010455:Peptides; D020543:Proteome; D014357:Trypsin