Fast and accurate identification of semi-tryptic peptides in shotgun proteomics.
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.
Alves
Pedro
P
School of Informatics, Bloomington, IN, USA.
Arnold
Randy J
RJ
Clemmer
David E
DE
Li
Yixue
Y
Reilly
James P
JP
Sheng
Quanhu
Q
Tang
Haixu
H
Xun
Zhiyin
Z
Zeng
Rong
R
Radivojac
Predrag
P
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*
D010455:Peptides; D020543:Proteome; D014357:Trypsin