PhosphoScore: an Open-source Phosphorylation Site Assignment Tool for MSn Data

Overview

Journal J Proteome Res

Publisher American Chemical Society

Specialty Biochemistry

Date 2008 Jun 12

PMID 18543960

Citations 41

Authors

Brian E Ruttenberg

Trairak Pisitkun

Mark A Knepper

Jason D Hoffert

Affiliations

Soon will be listed here.

Abstract

Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To this end, we have created PhosphoScore, an open-source assignment program that is compatible with phosphopeptide data from multiple MS levels (MS(n)). The algorithm takes into account both the match quality and normalized intensity of observed spectral peaks compared to a theoretical spectrum. PhosphoScore produced >95% correct MS(2) assignments from known synthetic data, > 98% agreement with an established MS(2) assignment algorithm (Ascore), and >92% agreement with visual inspection of MS(3) and MS(4) spectra.

Citing Articles

Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification.

Muneer G, Chen C, Chen Y Proteomics. 2024; 25(1-2):e202400087.

PMID: 39696887 PMC: 11735659. DOI: 10.1002/pmic.202400087.

Cholesterol Regulates the Tumor Adaptive Resistance to MAPK Pathway Inhibition.

Wang X, Kim C, Zhang Y, Rindhe S, Cobb M, Yu Y J Proteome Res. 2021; 20(12):5379-5391.

PMID: 34751028 PMC: 8905657. DOI: 10.1021/acs.jproteome.1c00550.

Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging.

Liu X, Fields R, Schweppe D, Paulo J Expert Rev Proteomics. 2021; 18(9):795-807.

PMID: 34652972 PMC: 8595857. DOI: 10.1080/14789450.2021.1994390.

Advances in quantitative high-throughput phosphoproteomics with sample multiplexing.

Paulo J, Schweppe D Proteomics. 2021; 21(9):e2000140.

PMID: 33455035 PMC: 8209658. DOI: 10.1002/pmic.202000140.

PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome.

An Z, Zhai L, Ying W, Qian X, Gong F, Tan M Mol Cell Proteomics. 2018; 18(2):391-405.

PMID: 30420486 PMC: 6356076. DOI: 10.1074/mcp.RA118.000812.

References

Molina H, Horn D, Tang N, Mathivanan S, Pandey A . Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A. 2007; 104(7):2199-204. PMC: 1794346. DOI: 10.1073/pnas.0611217104. View

Eng J, McCormack A, Yates J . An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom. 2013; 5(11):976-89. DOI: 10.1016/1044-0305(94)80016-2. View

Hoffert J, Wang G, Pisitkun T, Shen R, Knepper M . An automated platform for analysis of phosphoproteomic datasets: application to kidney collecting duct phosphoproteins. J Proteome Res. 2007; 6(9):3501-8. PMC: 2481407. DOI: 10.1021/pr0701153. View

Lu B, Ruse C, Xu T, Park S, Yates 3rd J . Automatic validation of phosphopeptide identifications from tandem mass spectra. Anal Chem. 2007; 79(4):1301-10. PMC: 2527591. DOI: 10.1021/ac061334v. View

Wolf-Yadlin A, Hautaniemi S, Lauffenburger D, White F . Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci U S A. 2007; 104(14):5860-5. PMC: 1851582. DOI: 10.1073/pnas.0608638104. View

Gruhler A, Olsen J, Mohammed S, Mortensen P, Faergeman N, Mann M . Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics. 2005; 4(3):310-27. DOI: 10.1074/mcp.M400219-MCP200. View

Olsen J, Mann M . Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A. 2004; 101(37):13417-22. PMC: 518757. DOI: 10.1073/pnas.0405549101. View

Beausoleil S, Jedrychowski M, Schwartz D, Elias J, Villen J, Li J . Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci U S A. 2004; 101(33):12130-5. PMC: 514446. DOI: 10.1073/pnas.0404720101. View

Geman S, Geman D . Stochastic relaxation, gibbs distributions, and the bayesian restoration of images. IEEE Trans Pattern Anal Mach Intell. 2012; 6(6):721-41. DOI: 10.1109/tpami.1984.4767596. View

10.

Bafna V, Edwards N . SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. Bioinformatics. 2001; 17 Suppl 1:S13-21. DOI: 10.1093/bioinformatics/17.suppl_1.s13. View

11.

Beausoleil S, Villen J, Gerber S, Rush J, Gygi S . A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol. 2006; 24(10):1285-92. DOI: 10.1038/nbt1240. View

12.

Wan Y, Yang A, Chen T . PepHMM: a hidden Markov model based scoring function for mass spectrometry database search. Anal Chem. 2006; 78(2):432-7. DOI: 10.1021/ac051319a. View

13.

Cantin G, Venable J, Cociorva D, Yates 3rd J . Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway. J Proteome Res. 2006; 5(1):127-34. PMC: 2570265. DOI: 10.1021/pr050270m. View

14.

Hoffert J, Pisitkun T, Wang G, Shen R, Knepper M . Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites. Proc Natl Acad Sci U S A. 2006; 103(18):7159-64. PMC: 1459033. DOI: 10.1073/pnas.0600895103. View

15.

Olsen J, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P . Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell. 2006; 127(3):635-48. DOI: 10.1016/j.cell.2006.09.026. View