Separating the Wheat from the Chaff: Unbiased Filtering of Background Tandem Mass Spectra Improves Protein Identification

Overview

Journal J Proteome Res

Publisher American Chemical Society

Specialty Biochemistry

Date 2008 Jun 19

PMID 18558732

Citations 17

Authors

Magno Junqueira

Victor Spirin

Tiago Santana Balbuena

Patrice Waridel

Vineeth Surendranath

Grigoriy Kryukov

Ivan Adzhubei

Henrik Thomas

Shamil Sunyaev

Andrej Shevchenko

Affiliations

Soon will be listed here.

Abstract

Only a small fraction of spectra acquired in LC-MS/MS runs matches peptides from target proteins upon database searches. The remaining, operationally termed background, spectra originate from a variety of poorly controlled sources and affect the throughput and confidence of database searches. Here, we report an algorithm and its software implementation that rapidly removes background spectra, regardless of their precise origin. The method estimates the dissimilarity distance between screened MS/MS spectra and unannotated spectra from a partially redundant background library compiled from several control and blank runs. Filtering MS/MS queries enhanced the protein identification capacity when searches lacked spectrum to sequence matching specificity. In sequence-similarity searches it reduced by, on average, 30-fold the number of orphan hits, which were not explicitly related to background protein contaminants and required manual validation. Removing high quality background MS/MS spectra, while preserving in the data set the genuine spectra from target proteins, decreased the false positive rate of stringent database searches and improved the identification of low-abundance proteins.

Citing Articles

Bipartite graphs in systems biology and medicine: a survey of methods and applications.

Pavlopoulos G, Kontou P, Pavlopoulou A, Bouyioukos C, Markou E, Bagos P Gigascience. 2018; 7(4):1-31.

PMID: 29648623 PMC: 6333914. DOI: 10.1093/gigascience/giy014.

Systematic Errors in Peptide and Protein Identification and Quantification by Modified Peptides.

Bogdanow B, Zauber H, Selbach M Mol Cell Proteomics. 2016; 15(8):2791-801.

PMID: 27215553 PMC: 4974352. DOI: 10.1074/mcp.M115.055103.

Genome-wide association study identifies common genetic variants associated with salivary gland carcinoma and its subtypes.

Xu L, Tang H, Chen D, El-Naggar A, Wei P, Sturgis E Cancer. 2015; 121(14):2367-74.

PMID: 25823930 PMC: 4564998. DOI: 10.1002/cncr.29381.

Displacement-weighted velocity analysis of gliding assays reveals that Chlamydomonas axonemal dynein preferentially moves conspecific microtubules.

Alper J, Tovar M, Howard J Biophys J. 2013; 104(9):1989-98.

PMID: 23663842 PMC: 3647177. DOI: 10.1016/j.bpj.2013.03.041.

One-step purification of assembly-competent tubulin from diverse eukaryotic sources.

Widlund P, Podolski M, Reber S, Alper J, Storch M, Hyman A Mol Biol Cell. 2012; 23(22):4393-401.

PMID: 22993214 PMC: 3496613. DOI: 10.1091/mbc.E12-06-0444.

References

Shevchenko A, Chernushevic I, Shevchenko A, Wilm M, Mann M . "De novo" sequencing of peptides recovered from in-gel digested proteins by nanoelectrospray tandem mass spectrometry. Mol Biotechnol. 2002; 20(1):107-18. DOI: 10.1385/mb:20:1:107. View

Shevchenko A, Chernushevich I, Ens W, Standing K, Thomson B, Wilm M . Rapid 'de novo' peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer. Rapid Commun Mass Spectrom. 1997; 11(9):1015-24. DOI: 10.1002/(SICI)1097-0231(19970615)11:9<1015::AID-RCM958>3.0.CO;2-H. View

Shevchenko A, de Sousa M, Waridel P, Bittencourt S, de Sousa M, Shevchenko A . Sequence similarity-based proteomics in insects: characterization of the larvae venom of the Brazilian moth Cerodirphia speciosa. J Proteome Res. 2005; 4(3):862-9. DOI: 10.1021/pr0500051. View

Medzihradszky K, Campbell J, Baldwin M, Falick A, Juhasz P, Vestal M . The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal Chem. 2000; 72(3):552-8. DOI: 10.1021/ac990809y. View

Schaefer H, Chamrad D, Marcus K, Reidegeld K, Bluggel M, Meyer H . Tryptic transpeptidation products observed in proteome analysis by liquid chromatography-tandem mass spectrometry. Proteomics. 2005; 5(4):846-52. DOI: 10.1002/pmic.200401203. View

Venable J, Dong M, Wohlschlegel J, Dillin A, Yates J . Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods. 2005; 1(1):39-45. DOI: 10.1038/nmeth705. View

Stein S, Scott D . Optimization and testing of mass spectral library search algorithms for compound identification. J Am Soc Mass Spectrom. 2013; 5(9):859-66. DOI: 10.1016/1044-0305(94)87009-8. View

Chalkley R, Baker P, Huang L, Hansen K, Allen N, Rexach M . Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: II. New developments in Protein Prospector allow for.... Mol Cell Proteomics. 2005; 4(8):1194-204. DOI: 10.1074/mcp.D500002-MCP200. View

Taylor J, Johnson R . Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem. 2001; 73(11):2594-604. DOI: 10.1021/ac001196o. View

10.

Liska A, Popov A, Sunyaev S, Coughlin P, Habermann B, Shevchenko A . Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome. Proteomics. 2004; 4(9):2707-21. DOI: 10.1002/pmic.200300813. View

11.

Sunyaev S, Liska A, Golod A, Shevchenko A, Shevchenko A . MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry. Anal Chem. 2003; 75(6):1307-15. DOI: 10.1021/ac026199a. View

12.

Habermann B, Oegema J, Sunyaev S, Shevchenko A . The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches. Mol Cell Proteomics. 2003; 3(3):238-49. DOI: 10.1074/mcp.M300073-MCP200. View

13.

Elias J, Gygi S . Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods. 2007; 4(3):207-14. DOI: 10.1038/nmeth1019. View

14.

Katz A, Waridel P, Shevchenko A, Pick U . Salt-induced changes in the plasma membrane proteome of the halotolerant alga Dunaliella salina as revealed by blue native gel electrophoresis and nano-LC-MS/MS analysis. Mol Cell Proteomics. 2007; 6(9):1459-72. DOI: 10.1074/mcp.M700002-MCP200. View

15.

Savitski M, Nielsen M, Zubarev R . New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques. Mol Cell Proteomics. 2005; 4(8):1180-8. DOI: 10.1074/mcp.T500009-MCP200. View

16.

Waridel P, Frank A, Thomas H, Surendranath V, Sunyaev S, Pevzner P . Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing. Proteomics. 2007; 7(14):2318-29. DOI: 10.1002/pmic.200700003. View

17.

Mackey A, Haystead T, Pearson W . Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences. Mol Cell Proteomics. 2002; 1(2):139-47. DOI: 10.1074/mcp.m100004-mcp200. View

18.

Loboda , Krutchinsky , Bromirski , Ens , Standing . A tandem quadrupole/time-of-flight mass spectrometer with a matrix-assisted laser desorption/ionization source: design and performance. Rapid Commun Mass Spectrom. 2000; 14(12):1047-57. DOI: 10.1002/1097-0231(20000630)14:12<1047::AID-RCM990>3.0.CO;2-E. View

19.

Wielsch N, Thomas H, Surendranath V, Waridel P, Frank A, Pevzner P . Rapid validation of protein identifications with the borderline statistical confidence via de novo sequencing and MS BLAST searches. J Proteome Res. 2006; 5(9):2448-56. DOI: 10.1021/pr060200v. View

20.

Chalkley R, Baker P, Hansen K, Medzihradszky K, Allen N, Rexach M . Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: I. How much of the data is theoretically interpretable by.... Mol Cell Proteomics. 2005; 4(8):1189-93. DOI: 10.1074/mcp.D500001-MCP200. View