ProSight PTM 2.0: Improved Protein Identification and Characterization for Top Down Mass Spectrometry

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2007 Jun 26

PMID 17586823

Citations 119

Authors

Leonid Zamdborg

Richard D LeDuc

Kevin J Glowacz

Yong-Bin Kim

Vinayak Viswanathan

Ian T Spaulding

Bryan P Early

Eric J Bluhm

Shannee Babai

Neil L Kelleher

Affiliations

Soon will be listed here.

Abstract

ProSight PTM 2.0 (http://prosightptm2.scs.uiuc.edu) is the next generation of the ProSight PTM web-based system for the identification and characterization of proteins using top down tandem mass spectrometry. It introduces an entirely new data-driven interface, integrated Sequence Gazer for protein characterization, support for fixed modifications, terminal modifications and improved support for multiple precursor ions (multiplexing). Furthermore, it supports data import and export for local analysis and collaboration.

Citing Articles

Proteoform identification using multiplexed top-down mass spectra.

Wang Z, Xiong X, Liu X bioRxiv. 2025; .

PMID: 39975217 PMC: 11839095. DOI: 10.1101/2025.02.05.636727.

FAST MS: Software for the Automated Analysis of Top-Down Mass Spectra of Polymeric Molecules Including RNA, DNA, and Proteins.

Palasser M, Breuker K J Am Soc Mass Spectrom. 2024; 36(2):247-257.

PMID: 39715325 PMC: 11808778. DOI: 10.1021/jasms.4c00236.

Top-down proteomics.

Roberts D, Loo J, Tsybin Y, Liu X, Wu S, Chamot-Rooke J Nat Rev Methods Primers. 2024; 4(1).

PMID: 39006170 PMC: 11242913. DOI: 10.1038/s43586-024-00318-2.

Direct Identification of Intact Proteins Using a Low-Resolution Mass Spectrometer with CID/ETnoD.

Kuo C, Zheng Y, Wang W, Toh J, Hsu Y, Chien H J Am Soc Mass Spectrom. 2024; 35(7):1507-1515.

PMID: 38905484 PMC: 11228978. DOI: 10.1021/jasms.4c00108.

Top-down mass spectrometry of native proteoforms and their complexes: a community study.

Habeck T, Brown K, Des Soye B, Lantz C, Zhou M, Alam N Nat Methods. 2024; 21(12):2388-2396.

PMID: 38744918 PMC: 11561160. DOI: 10.1038/s41592-024-02279-6.

References

Fenn J . Ion formation from charged droplets: Roles of geometry, energy, and time. J Am Soc Mass Spectrom. 2013; 4(7):524-35. DOI: 10.1016/1044-0305(93)85014-O. View

Johnson J, Meng F, Forbes A, Cargile B, Kelleher N . Fourier-transform mass spectrometry for automated fragmentation and identification of 5-20 kDa proteins in mixtures. Electrophoresis. 2002; 23(18):3217-23. DOI: 10.1002/1522-2683(200209)23:18<3217::AID-ELPS3217>3.0.CO;2-K. View

Mann M, Wilm M . Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem. 1994; 66(24):4390-9. DOI: 10.1021/ac00096a002. View

Washburn M, Yates 3rd J . Analysis of the microbial proteome. Curr Opin Microbiol. 2000; 3(3):292-7. DOI: 10.1016/s1369-5274(00)00092-8. View

Pesavento J, Kim Y, Taylor G, Kelleher N . Shotgun annotation of histone modifications: a new approach for streamlined characterization of proteins by top down mass spectrometry. J Am Chem Soc. 2004; 126(11):3386-7. PMC: 1343470. DOI: 10.1021/ja039748i. View

Meng F, Cargile B, Miller L, Forbes A, Johnson J, Kelleher N . Informatics and multiplexing of intact protein identification in bacteria and the archaea. Nat Biotechnol. 2001; 19(10):952-7. DOI: 10.1038/nbt1001-952. View

LeDuc R, Kelleher N . Using ProSight PTM and related tools for targeted protein identification and characterization with high mass accuracy tandem MS data. Curr Protoc Bioinformatics. 2008; Chapter 13:Unit 13.6. DOI: 10.1002/0471250953.bi1306s19. View

Horn D, Zubarev R, McLafferty F . Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J Am Soc Mass Spectrom. 2000; 11(4):320-32. DOI: 10.1016/s1044-0305(99)00157-9. View

Karchin R, Diekhans M, Kelly L, Thomas D, Pieper U, Eswar N . LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics. 2005; 21(12):2814-20. DOI: 10.1093/bioinformatics/bti442. View

10.

Mann M, Jensen O . Proteomic analysis of post-translational modifications. Nat Biotechnol. 2003; 21(3):255-61. DOI: 10.1038/nbt0303-255. View

11.

Roth M, Forbes A, Boyne 2nd M, Kim Y, Robinson D, Kelleher N . Precise and parallel characterization of coding polymorphisms, alternative splicing, and modifications in human proteins by mass spectrometry. Mol Cell Proteomics. 2005; 4(7):1002-8. PMC: 1307493. DOI: 10.1074/mcp.M500064-MCP200. View

12.

LeDuc R, Taylor G, Kim Y, Januszyk T, Bynum L, Sola J . ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry. Nucleic Acids Res. 2004; 32(Web Server issue):W340-5. PMC: 441585. DOI: 10.1093/nar/gkh447. View

13.

Smigielski E, Sirotkin K, Ward M, Sherry S . dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res. 1999; 28(1):352-5. PMC: 102496. DOI: 10.1093/nar/28.1.352. View

14.

Zabrouskov V, Senko M, Du Y, LeDuc R, Kelleher N . New and automated MSn approaches for top-down identification of modified proteins. J Am Soc Mass Spectrom. 2005; 16(12):2027-38. PMC: 3803164. DOI: 10.1016/j.jasms.2005.08.004. View

15.

Reid G, Shang H, Hogan J, Lee G, McLuckey S . Gas-phase concentration, purification, and identification of whole proteins from complex mixtures. J Am Chem Soc. 2002; 124(25):7353-62. DOI: 10.1021/ja025966k. View

16.

Ficarro S, McCleland M, Stukenberg P, Burke D, Ross M, Shabanowitz J . Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol. 2002; 20(3):301-5. DOI: 10.1038/nbt0302-301. View

17.

Garavelli J, Hou Z, Pattabiraman N, Stephens R . The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database. Nucleic Acids Res. 2000; 29(1):199-201. PMC: 29832. DOI: 10.1093/nar/29.1.199. View

18.

Senko M, Canterbury J, Guan S, G Marshall A . A high-performance modular data system for Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom. 1996; 10(14):1839-44. DOI: 10.1002/(SICI)1097-0231(199611)10:14<1839::AID-RCM718>3.0.CO;2-V. View