SQID: an intensity-incorporated protein identification algorithm for tandem mass spectrometry.

ABSTRACT: To interpret LC-MS/MS data in proteomics, most popular protein identification algorithms primarily use predicted fragment m/z values to assign peptide sequences to fragmentation spectra. The intensity information is often undervalued, because it is not as easy to predict and incorporate into algorithms. Nevertheless, the use of intensity to assist peptide identification is an attractive prospect and can potentially improve the confidence of matches and generate more identifications. On the basis of our previously reported study of fragmentation intensity patterns, we developed a protein identification algorithm, SeQuence IDentfication (SQID), that makes use of the coarse intensity from a statistical analysis. The scoring scheme was validated by comparing with Sequest and X!Tandem using thr

SUBMITTER: Li W 

PROVIDER: S-EPMC3477243 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature