Software:PeptideSieve

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Revision as of 03:49, 8 October 2007; view current revision
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Peptide Sieve Package & Server

1 Description
2 Method outline
3 Reference
4 Getting the software
5 Predictions and Supplementary Materials

Description

It has been noted [1] that only a handful of a protein’s possible tryptic peptides are consistently observed in proteomics experiments. We denote these consistently observed peptides to be proteotypic peptides. Such peptides have a variety of potential applications in proteomic research including improving protein identification scoring functions of database search software, providing a panel of reagents for protein quantification as well as the annotation of genomes for coding sequences of e.g. the hundreds of sequenced bacterial genomes some of which are important model organisms in systems biology and a guide for peptide selection in targeted proteomics experiments. Here we present PeptideSieve, an alpha version of a computational tool to predict a peptide’s proteotypic propensity based on its physico-chemical properties. The resulting predictors have the ability to accurately identify proteotypic peptides from any protein sequence and offer starting points for generating a physical model describing the factors that govern elements of proteomic workflows such as digestion, chromatography, ionization and fragmentation.

The software consists of a PERL program wrapping a C++ program. The input is a FASTA file of protein sequences and a parameter file. The program then returns which of a protein's peptides are most likely to be proteotypic for each of four common experimental designs. The PERL program is executed from the command line.

Method outline

The program first performs an in silico digest of the protein and then converts each of the peptides into chemical property strings. The C++ program then computes a likelihood function, which scores the likelihood each peptide is proteotypic. It is important to note that the predictors are specific for particular experimental designs.

Reference

[1] Nat Biotechnol. 2007 Jan;25(1):125-31. Computational prediction of proteotypic peptides for quantitative proteomics. Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R.

Getting the software

Notice: A new, re-written version of PeptideSieve will be released on or around October 8th 2007. This version fixes a known bug in converting some datasets, and will be available here as soon as it is released.

Current version (0.2a:) PeptideSieve_v0.2a.tgz

We are very pleased to present a GUI version of the software provided by Chee-Hong Wong (wongch at bii dot a-star dot edu dot sg)!

PeptideSieve_v0.2a.with.GUI.setup.exe: installer for windows executable
PeptideSieve_v0.2a.with.GUI.zip: source, including PeptideSieve_v0.2a.tgz with change to supportFunctions.pl, a PeptideSieve subfolder with VC++8 project files, a sample screen, a text based readme for the GUI, and a html file.