Literature DB >> 15215407

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

Richard D LeDuc1, Gregory K Taylor, Yong-Bin Kim, Thomas E Januszyk, Lee H Bynum, Joseph V Sola, John S Garavelli, Neil L Kelleher.   

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.

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Year:  2004        PMID： 15215407      PMCID： PMC441585          DOI： 10.1093/nar/gkh447

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  12 in total

1.  The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database.

Authors:  J S Garavelli; Z Hou; N Pattabiraman; R M Stephens
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

Review 2.  Analysis of the microbial proteome.

Authors:  M P Washburn; J R Yates
Journal:  Curr Opin Microbiol       Date:  2000-06       Impact factor: 7.934

3.  Informatics and multiplexing of intact protein identification in bacteria and the archaea.

Authors:  F Meng; B J Cargile; L M Miller; A J Forbes; J R Johnson; N L Kelleher
Journal:  Nat Biotechnol       Date:  2001-10       Impact factor: 54.908

Review 4.  Proteomic analysis of post-translational modifications.

Authors:  Matthias Mann; Ole N Jensen
Journal:  Nat Biotechnol       Date:  2003-03       Impact factor: 54.908

5.  The RESID Database of Protein Modifications: 2003 developments.

Authors:  John S Garavelli
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

6.  A high-performance modular data system for Fourier transform ion cyclotron resonance mass spectrometry.

Authors:  M W Senko; J D Canterbury; S Guan; A G Marshall
Journal:  Rapid Commun Mass Spectrom       Date:  1996       Impact factor: 2.419

7.  Error-tolerant identification of peptides in sequence databases by peptide sequence tags.

Authors:  M Mann; M Wilm
Journal:  Anal Chem       Date:  1994-12-15       Impact factor: 6.986

8.  Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite chromatography.

Authors:  M Fountoulakis; M F Takács; P Berndt; H Langen; B Takács
Journal:  Electrophoresis       Date:  1999-08       Impact factor: 3.535

9.  Processing complex mixtures of intact proteins for direct analysis by mass spectrometry.

Authors:  Fanyu Meng; Benjamin J Cargile; Steven M Patrie; Jeffrey R Johnson; Shaun M McLoughlin; Neil L Kelleher
Journal:  Anal Chem       Date:  2002-07-01       Impact factor: 6.986

10.  Web and database software for identification of intact proteins using "top down" mass spectrometry.

Authors:  Gregory K Taylor; Yong-Bin Kim; Andrew J Forbes; Fanyu Meng; Ryan McCarthy; Neil L Kelleher
Journal:  Anal Chem       Date:  2003-08-15       Impact factor: 6.986
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  80 in total

1.  A comprehensive pipeline for translational top-down proteomics from a single blood draw.

Authors:  Timothy K Toby; Luca Fornelli; Kristina Srzentić; Caroline J DeHart; Josh Levitsky; John Friedewald; Neil L Kelleher
Journal:  Nat Protoc       Date:  2019-01       Impact factor: 13.491

2.  Protein identification using top-down.

Authors:  Xiaowen Liu; Yakov Sirotkin; Yufeng Shen; Gordon Anderson; Yihsuan S Tsai; Ying S Ting; David R Goodlett; Richard D Smith; Vineet Bafna; Pavel A Pevzner
Journal:  Mol Cell Proteomics       Date:  2011-10-25       Impact factor: 5.911

3.  Defining intact protein primary structures from saliva: a step toward the human proteome project.

Authors:  F Halgand; V Zabrouskov; S Bassilian; P Souda; J A Loo; K F Faull; D T Wong; J P Whitelegge
Journal:  Anal Chem       Date:  2012-05-02       Impact factor: 6.986

4.  MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics.

Authors:  Wenxuan Cai; Huseyin Guner; Zachery R Gregorich; Albert J Chen; Serife Ayaz-Guner; Ying Peng; Santosh G Valeja; Xiaowen Liu; Ying Ge
Journal:  Mol Cell Proteomics       Date:  2015-11-23       Impact factor: 5.911

5.  Characterization of a new qQq-FTICR mass spectrometer for post-translational modification analysis and top-down tandem mass spectrometry of whole proteins.

Authors:  Judith A Jebanathirajah; Jason L Pittman; Bruce A Thomson; Bogdan A Budnik; Parminder Kaur; Michael Rape; Marc Kirschner; Catherine E Costello; Peter B O'Connor
Journal:  J Am Soc Mass Spectrom       Date:  2005-11-02       Impact factor: 3.109

6.  New and automated MSn approaches for top-down identification of modified proteins.

Authors:  Vlad Zabrouskov; Michael W Senko; Yi Du; Richard D Leduc; Neil L Kelleher
Journal:  J Am Soc Mass Spectrom       Date:  2005-10-25       Impact factor: 3.109

7.  Evolutionary migration of a post-translationally modified active-site residue in the proton-pumping heme-copper oxygen reductases.

Authors:  James Hemp; Dana E Robinson; Krithika B Ganesan; Todd J Martinez; Neil L Kelleher; Robert B Gennis
Journal:  Biochemistry       Date:  2006-12-19       Impact factor: 3.162

8.  MassMatrix: a database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data.

Authors:  Hua Xu; Michael A Freitas
Journal:  Proteomics       Date:  2009-03       Impact factor: 3.984

Review 9.  Identification and Quantification of Proteoforms by Mass Spectrometry.

Authors:  Leah V Schaffer; Robert J Millikin; Rachel M Miller; Lissa C Anderson; Ryan T Fellers; Ying Ge; Neil L Kelleher; Richard D LeDuc; Xiaowen Liu; Samuel H Payne; Liangliang Sun; Paul M Thomas; Trisha Tucholski; Zhe Wang; Si Wu; Zhijie Wu; Dahang Yu; Michael R Shortreed; Lloyd M Smith
Journal:  Proteomics       Date:  2019-05       Impact factor: 3.984

Review 10.  Top Down proteomics: facts and perspectives.

Authors:  Adam D Catherman; Owen S Skinner; Neil L Kelleher
Journal:  Biochem Biophys Res Commun       Date:  2014-02-17       Impact factor: 3.575
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