By Amit K. Yadav (
@theoneamit) & Yasset Perez-Riverol (
@ypriverol):
Perl is a legacy language thought to be abstruse by many modern programmers. I’m passionate with the idea of not letting die a programming language such as Perl. Even when the language is used less in Computational Proteomics, it is still widely used in Bioinformatics. I’m enthusiastic writing about new open-source libraries in Perl that can be easily used. Two years ago, I wrote a post about
InSilicoSpectro and how it can be used to study protein databases like I did in “
In silico analysis of accurate proteomics, complemented by selective isolation of peptides”.
Today’s post is about
ProteoStats [
1], a Perl library for False Discovery Rate (FDR) related calculations in proteomics studies. Some background for non-experts:
One of the central and most widely used approach for shotgun proteomics is the use of database search tools to assign spectra to peptides (called as Peptide Spectrum Matches or PSMs). To evaluate the quality of the assignments, these programs need to calculate/correct for population wise error rates to keep the number of false positives under control. In that sense, the best strategy to control the false positives is the target-decoy approach. Originally proposed by Elias & Gygi in 2007, the so-called classical FDR strategy or formula proposed involved a concatenated target-decoy (TD) database search for FDR estimation. This calculation is either done by the search engine or using scripts (in-house, non-published, not benchmarked, different implementations).
So far, the only library developed to compute FDR at spectra level, peptide level and protein level FDRs is
MAYU [
2]. But, while MAYU only uses the classical FDR approach, ProteoStats provides options for 5 different strategies for calculating the FDR. The only prerequisite being that you need to search using a separate TD database as proposed by Kall et al (2008) [
3]. Also, ProteoStats provides a programming interface that can read the native output from most widely used search tools and provide FDR related statistics. In case of tools not supported,
pepXML, which has become a de facto standard output format, can be directly read along with tabular text based formats like TSV and CSV (or any other well-defined separator).
