UNLABELLED
Peptide-based proteomics supports identification and quantification as well as localization of post-translational modifications (PTMs) within proteins extracted from biological samples. The 'bottom-up' approach involves the digestion of proteins into peptide fragments that can be detected and sequenced with liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). A web-based application, iPEP, was developed to compare the effectiveness of different proteolytic digests in detecting specific sequences. Furthermore, peptide populations can be examined to help optimize detection of certain groups of proteins relative to the proteome and the digested peptidome. The application reports proteolytic peptide sequences, theoretical molecular weights and functional annotations using Gene Ontology (GO) terms. The iPEP tool can assist with experimental design by maximizing the detection of proteins, consensus sites and modified residues of interest for individual proteins or as part of large-scale proteomic assays.
AVAILABILITY
http://ipep.moffitt.org
[1]
Andrew Emili,et al.
In silico proteome analysis to facilitate proteomics experiments using mass spectrometry
,
2003,
Proteome Science.
[2]
Frank Fischer,et al.
Toward the Complete Membrane Proteome
,
2006,
Molecular & Cellular Proteomics.
[3]
Amos Bairoch,et al.
The PROSITE database
,
2005,
Nucleic Acids Res..
[4]
Tao Chen,et al.
GOFFA: Gene Ontology For Functional Analysis – A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data
,
2006,
BMC Bioinformatics.
[5]
Richard D. Smith,et al.
The Utility of Accurate Mass and LC Elution Time Information in the Analysis of Complex Proteomes
,
2005,
Journal of the American Society for Mass Spectrometry.