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

Introduction

pAnno^® is a proteogenomic tool that combines the following functions, (i) browsing genome, (ii) constructing a 6 frame translation protein database for MS/MS identification, (iii) using MS/MS searching result to re-annotate genome.

Database searching-based computational proteomics rely heavily on the completeness and accuracy of the protein sequences, but the protein sequences are not perfect (protein sequences are missing, translation initiation sites are mis-annotated), under which situation we need protegenomic searching. The imperfectness of the protein sequence could be refined by the original genome. Mapping MS/MS spectra to a protein database derived from 6 frame translation to some extent, could be a good solution. However, too much attention should be paid when using this technique, that is, novel PSMs may be false positives. To overcome this problem, we integrate a ORF (generated by 6 frame translation) level scoring strategy into pAnno, and give each ORF a local FDR value. This value could guide users to do further validations.

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