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

Richard D. LeDuc; Gregory K. Taylor; Yong Bin Kim; Thomas E. Januszyk; Lee H. Bynum; Joseph V. Sola; John S. Garavelli; Neil L. Kelleher

doi:10.1093/nar/gkh447

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

Richard D. LeDuc, Gregory K. Taylor, Yong Bin Kim, Thomas E. Januszyk, Lee H. Bynum, Joseph V. Sola, John S. Garavelli, Neil L. Kelleher^*

^*Corresponding author for this work

Molecular Biosciences

Research output: Contribution to journal › Article › peer-review

172 Scopus citations

Abstract

ProSight PTM (https://prosightptm.scs.uiuc.edu/) is a web application for identification and characterization of proteins using mass spectra data from 'topdown' 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.

Original language	English (US)
Pages (from-to)	W340-W345
Journal	Nucleic acids research
Volume	32
Issue number	WEB SERVER ISS.
DOIs	https://doi.org/10.1093/nar/gkh447
State	Published - Jul 1 2004

ASJC Scopus subject areas

Genetics

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title = "ProSight PTM: An integrated environment for protein identification and characterization by top-down mass spectrometry",

abstract = "ProSight PTM (https://prosightptm.scs.uiuc.edu/) is a web application for identification and characterization of proteins using mass spectra data from 'topdown' 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.",

author = "LeDuc, {Richard D.} and Taylor, {Gregory K.} and Kim, {Yong Bin} and Januszyk, {Thomas E.} and Bynum, {Lee H.} and Sola, {Joseph V.} and Garavelli, {John S.} and Kelleher, {Neil L.}",

note = "Funding Information: We thank these sources of support: the Searle Scholars Program Foundation, the Burroughs Wellcome Fund, the University of Illinois, the Packard Foundation and the National Institutes of Health (GM 067193).",

year = "2004",

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doi = "10.1093/nar/gkh447",

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AU - LeDuc, Richard D.

AU - Taylor, Gregory K.

AU - Kim, Yong Bin

AU - Januszyk, Thomas E.

AU - Bynum, Lee H.

AU - Sola, Joseph V.

AU - Garavelli, John S.

AU - Kelleher, Neil L.

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

Abstract

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