GAPP:  A Fully Automated Software for the Confident Identification of Human Peptides from Tandem Mass Spectra

Abstract

This paper introduces the genome annotating proteomic pipeline (GAPP), a totally automated publicly available software pipeline for the identification of peptides and proteins from human proteomic tandem mass spectrometry data. The pipeline takes as its input a series of MS/MS peak lists from a given experimental sample and produces a series of database entries corresponding to the peptides observed within the sample, along with related confidence scores. The pipeline is capable of finding any peptides expected, including those that cross intron-exon boundaries, and those due to single nucleotide polymorphisms (SNPs), alternate splicing, and post-translational modifications (PTMs). GAPP can therefore be used to re-annotate genomes, and this is supported through the inclusion of a Distributed Annotation System (DAS) server, which allows the peptides identified by the pipeline to be displayed in their genomic context within the Ensembl genome browser. GAPP is freely available via the web, at www. gapp.info.

MRMaid, the Web-based Tool for Designing Multiple Reaction Monitoring (MRM) Transitions

“…The MRMaid method for transition design relies on the combination of two sources of information: first on prior knowledge of the kind of precursor peptides that generally perform better in MS/MS and second on mining the data in a proteomics data repository, Genome Annotating Proteomic Pipeline (GAPP) (19), to determine which precursor and corresponding fragment ions have appeared regularly for the given protein of interest. The hydrophobicity and RP RT of each peptide candidate are calculated so suitable transitions may be selected and ordered.…”

Applications of selected reaction monitoring (SRM)-mass spectrometry (MS) for quantitative measurement of signaling pathways

“…The MS/MS spectra of proteotypic peptides generated by laboratories world-wide have been collected empirically in public proteomics repository databases, such as PeptideAtlas (http://www.peptideatlas.org), Global Proteome Machine Database (GPMDB) (http://gpmdb.thegpm.org), the Public Repository of Protein and Peptide Identifications (PRIDE) (http://www.ebi.ac.uk/pride), and Genome Annotating Proteome Pipeline (GAPP) (http://www.gapp.info/) [21–24]. The information in these databases has been successfully used for selecting high-responding signature peptides [25–27].…”

MRMaid 2.0: Mining PRIDE for Evidence-Based SRM Transitions

“…The spectral data and related metadata for the mapped proteotypic peptides are retrieved from the public PRIDE MySQL database. In the original MRMaid we used a relatively small but high quality in-house spectral dataset generated by our GAPP identification pipeline (Shadforth et al, 2006). Moving to the PRIDE database gives us access to several orders of magnitude more spectra, but quality is not guaranteed, as the majority of data in PRIDE are not curated.…”