ProSight Lite: Graphical Software to Analyze Top-down Mass Spectrometry Data

Overview

Journal Proteomics

Date 2015 Apr 2

PMID 25828799

Citations 135

Authors

Ryan T Fellers

Joseph B Greer

Bryan P Early

Xiang Yu

Richard D LeDuc

Neil L Kelleher

Paul M Thomas

Affiliations

Soon will be listed here.

Abstract

Many top-down proteomics experiments focus on identifying and localizing PTMs and other potential sources of “mass shift” on a known protein sequence. A simple application to match ion masses and facilitate the iterative hypothesis testing of PTM presence and location would assist with the data analysis in these experiments. ProSight Lite is a free software tool for matching a single candidate sequence against a set of mass spectrometric observations. Fixed or variable modifications, including both PTMs and a select number of glycosylations, can be applied to the amino acid sequence. The application reports multiple scores and a matching fragment list. Fragmentation maps can be exported for publication in either portable network graphic (PNG) or scalable vector graphic (SVG) format. ProSight Lite can be freely downloaded from http://prosightlite.northwestern.edu, installs and updates from the web, and requires Windows 7 or a higher version.

Citing Articles

Tracking proteasome degradation: A cross-organ analysis via intact degradomics mass spectrometry.

Zittlau K, Zachor-Movshovitz D, Leushkin Y, Schimmel Brener R, Morgenstern D, Ben-Nissan G Proc Natl Acad Sci U S A. 2025; 122(8):e2419607122.

PMID: 39964708 PMC: 11874349. DOI: 10.1073/pnas.2419607122.

Deciphering the safeguarding role of cysteine residues in p53 against HO-induced oxidation using high-resolution native mass spectrometry.

Peris-Diaz M, Krezel A, Barran P Commun Chem. 2025; 8(1):13.

PMID: 39814824 PMC: 11736120. DOI: 10.1038/s42004-024-01395-w.

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.

Quantitative Top-down Proteomics Revealed Kinase Inhibitor-Induced Proteoform-Level Changes in Cancer Cells.

Chowdhury T, Cupp-Sutton K, Guo Y, Gao K, Zhao Z, Burgett A J Proteome Res. 2024; 24(1):303-314.

PMID: 39620430 PMC: 11784628. DOI: 10.1021/acs.jproteome.4c00778.

A Conformation-Specific Approach to Native Top-down Mass Spectrometry.

Britt H, Ben-Younis A, Page N, Thalassinos K J Am Soc Mass Spectrom. 2024; 35(12):3203-3213.

PMID: 39453623 PMC: 11622372. DOI: 10.1021/jasms.4c00361.

References

Cui W, Rohrs H, Gross M . Top-down mass spectrometry: recent developments, applications and perspectives. Analyst. 2011; 136(19):3854-64. PMC: 3505190. DOI: 10.1039/c1an15286f. View

Siuti N, Kelleher N . Decoding protein modifications using top-down mass spectrometry. Nat Methods. 2007; 4(10):817-21. PMC: 2365886. DOI: 10.1038/nmeth1097. View

Zamdborg L, LeDuc R, Glowacz K, Kim Y, Viswanathan V, Spaulding I . ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry. Nucleic Acids Res. 2007; 35(Web Server issue):W701-6. PMC: 1933126. DOI: 10.1093/nar/gkm371. View

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

Kelleher N . Top-down proteomics. Anal Chem. 2004; 76(11):197A-203A. View

Tyers M, Mann M . From genomics to proteomics. Nature. 2003; 422(6928):193-7. DOI: 10.1038/nature01510. 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

Horn D, Ge Y, McLafferty F . Activated ion electron capture dissociation for mass spectral sequencing of larger (42 kDa) proteins. Anal Chem. 2000; 72(20):4778-84. DOI: 10.1021/ac000494i. 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

10.

Dang X, Scotcher J, Wu S, Chu R, Tolic N, Ntai I . The first pilot project of the consortium for top-down proteomics: a status report. Proteomics. 2014; 14(10):1130-40. PMC: 4146406. DOI: 10.1002/pmic.201300438. View

11.

Campbell M, Peterson R, Mariethoz J, Gasteiger E, Akune Y, Aoki-Kinoshita K . UniCarbKB: building a knowledge platform for glycoproteomics. Nucleic Acids Res. 2013; 42(Database issue):D215-21. PMC: 3964942. DOI: 10.1093/nar/gkt1128. View

12.

Shaw J, Li W, Holden D, Zhang Y, Griep-Raming J, Fellers R . Complete protein characterization using top-down mass spectrometry and ultraviolet photodissociation. J Am Chem Soc. 2013; 135(34):12646-51. PMC: 3757099. DOI: 10.1021/ja4029654. View

13.

Smith L, Kelleher N . Proteoform: a single term describing protein complexity. Nat Methods. 2013; 10(3):186-7. PMC: 4114032. DOI: 10.1038/nmeth.2369. View

14.

Frese C, Altelaar A, van den Toorn H, Nolting D, Griep-Raming J, Heck A . Toward full peptide sequence coverage by dual fragmentation combining electron-transfer and higher-energy collision dissociation tandem mass spectrometry. Anal Chem. 2012; 84(22):9668-73. DOI: 10.1021/ac3025366. View

15.

Campbell M, Hayes C, Struwe W, Wilkins M, Aoki-Kinoshita K, Harvey D . UniCarbKB: putting the pieces together for glycomics research. Proteomics. 2011; 11(21):4117-21. DOI: 10.1002/pmic.201100302. View