ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry
Open Access
- 1 July 2004
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 32 (Web Server) , W340-W345
- https://doi.org/10.1093/nar/gkh447
Abstract
ProSight PTM (https://prosightptm.scs.uiuc.edu/) is a web application for identification and characterization of proteins using mass spectra data from ‘top-down’ fragmentation of intact protein ions (i.e. without any tryptic digestion). ProSight PTM has many tools and graphical features to facilitate analysis of single proteins, proteins in mixtures and proteins fragmented in parallel. Sequence databases from across the phylogenetic tree are supported, with a new database strategy of ‘shotgun annotation’ used to assist characterization of wild-type proteins. During a database search, data from divergent sources regarding potential mass differences such as polymorphisms, alternate splicing and post-translational modifications are utilized. The user can optionally control how much of this biological variability should be searched.Keywords
This publication has 11 references indexed in Scilit:
- Proteomic analysis of post-translational modificationsNature Biotechnology, 2003
- The RESID Database of Protein Modifications: 2003 developmentsNucleic Acids Research, 2003
- Processing Complex Mixtures of Intact Proteins for Direct Analysis by Mass SpectrometryAnalytical Chemistry, 2002
- Informatics and multiplexing of intact protein identification in bacteria and the archaeaNature Biotechnology, 2001
- The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure DatabaseNucleic Acids Research, 2001
- Analysis of the microbial proteomeCurrent Opinion in Microbiology, 2000
- Enrichment of low abundance proteins ofEscherichia coli by hydroxyapatite chromatographyElectrophoresis, 1999
- A High-performance Modular Data System for Fourier Transform Ion Cyclotron Resonance Mass SpectrometryRapid Communications in Mass Spectrometry, 1996
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence TagsAnalytical Chemistry, 1994
- Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequencesProteins-Structure Function and Bioinformatics, 1988