pFind Studio: a computational solution for mass spectrometry-based proteomics

Introduction

pFind^® 3 is developed as an upgrade of pFind 2.8 (visit the old version).

Shotgun proteomics has grown rapidly in recent decades, but a large fraction of tandem mass spectrometry data in shotgun proteomics are not successfully identified. Thus we developed a novel database search algorithm, Open-pFind, to efficiently identify peptides even in an ultra-large search space which takes into account unexpected modifications, amino acid mutations, semi- or non-specific digestion and co-eluting peptides. Open-pFind has now been integrated into pFind 3 as the default workflow, and pFind 3 also supports the restricted search mode, which can be switched in the interface.

Fig. 1. Workflow of Open-pFind, including the sub-workflow of the open search module. a) The workflow of Open-pFind. MS data are first preprocessed by pParse, and then the MS/MS data are searched by the open search module. Next, the MS data are re-searched by the restricted search module against the refined search space based on the learned information in the reranking step. Finally, the results obtained from both the open and restricted searches are merged, reranked again and reported. b) The default workflow of the open search module. For each spectrum, a few tags are extracted and then searched against the indexed protein database. Peptide candidates are then generated by extending the matched tags in proteins. Finally, peptides are scored with the spectrum and ranked; the mass shift between the precursor ion and each peptide is treated as a modification and localized by testing all valid positions.

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Copyright © pFind Team · Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China