ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry.

Nucleic acids research ·Vol. 32 ·No. Web Server issue ·2004-07-01 ·Pages W340-5

LeDuc RD, Taylor GK, Kim YB, Januszyk TE, Bynum LH, Sola JV, Garavelli JS, Kelleher NL

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.

MeSH Terms

Alternative Splicing Databases, Protein Humans Internet Mass Spectrometry Polymorphism, Genetic Protein Processing, Post-Translational Proteins/analysis,chemistry,genetics Ribosomal Proteins/chemistry Sequence Analysis, Protein Sequence Tagged Sites Software User-Computer Interface

Chemicals

Proteins RPS28 protein, human Ribosomal Proteins

Authors & Affiliations

8 authors, click to expand affiliations / ORCID

LeDuc Richard D

W.M. Keck Center for Comparative and Functional Genomics, University of Illinois, Urbana, IL 61801, USA.

Taylor Gregory K

Kim Yong-Bin

Januszyk Thomas E

Bynum Lee H

Sola Joseph V

Garavelli John S

Kelleher Neil L

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12 references, click to expand

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Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

1362-4962

DOI

10.1093/nar/gkh447

Published

2004-07-01

Pages

W340-5

Language

English

Region

England

NLM ID

0411011

PMCID

PMC441585

Subset

Grants

NIGMS NIH HHS · R01 GM067193 · United States

External Links

PubMed source DOI: 10.1093/nar/gkh447 PMC Full Text View journal details

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