Software:PeptideSieve

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Peptide Sieve Package & Server


Contents

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

New native C++ version released 10/29/2007 Download Build instructions for this version are available here.

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)!

Predictions and Supplementary Materials

AEBERSOLD_TABLE_S1_Observed_Proteins

AEBERSOLD_TABLE_S2_Proteotypic_Peptides

AEBERSOLD_TABLE_S7_PAGE_ESI

AEBERSOLD_TABLE_S8_CZ_MALDI

AEBERSOLD_TABLE_S9_MUDPIT

AEBERSOLD_TABLE_S10_MUDPIT

AEBERSOLD_TABLE_S11_YEAST_PREDICTIONS

AEBERSOLD_TABLE_S12_HUMAN_PREDICTIONS

AEBERSOLD_TABLE_S13_EXTENDED_YEAST_PREDICTIONS

AEBERSOLD_TABLE_S14_EXTENDED_HUMAN_PREDICTIONS

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