Open AccessProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry
Author(s) -
Richard D. LeDuc,
G. K. Taylor,
Yong Baek Kim,
T. E. Januszyk,
Lee Bynum,
Jordi Solà,
John S. Garavelli,
Neil L. Kelleher
Publication year - 2004
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gkh447
Subject(s) - biology , shotgun , computational biology , shotgun proteomics , mass spectrometry , identification (biology) , sequence database , annotation , database , genetics , bioinformatics , proteomics , gene , computer science , chemistry , chromatography , botany
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.
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