Review of peak detection algorithms in liquid-chromatography-mass spectrometry

Current Genomics

Volumn 10, Issue 6, 2009, Pages 388-401

  Zhang, Jianqiu ^a   Gonzalez, Elias ^a   Hestilow, Travis ^a   Haskins, William ^a   Huang, Yufei ^a,b  

^a UNIVERSITY OF TEXAS AT SAN ANTONIO   (United States)

^b UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; PEPTIDE;

ALGORITHM; ANALYTIC METHOD; COMPUTER PROGRAM; DATA ANALYSIS; ELUTION TIME; HUMAN; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR WEIGHT; NOISE REDUCTION; NORMAL DISTRIBUTION; PROBABILITY; PROTEIN ANALYSIS; QUANTITATIVE ANALYSIS; RECEIVER OPERATING CHARACTERISTIC; REVIEW; SIGNAL NOISE RATIO; SIGNAL PROCESSING; TIME; TIME OF FLIGHT MASS SPECTROMETRY;

EID: 70549106483     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920209789177638     Document Type: Review

References (41)

1. Tyers, M.; Mann, M. From genomics to proteomics. Nature, 2003, 422(6928), 193-197.
2. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature, 2003, 422(6928), 198-207.
3. Hanash, S. Disease proteomics. Nature, 2003, 422(6928), 226-232.
4. Boguski, M.S.; McIntosh, M.W. Biomedical informatics for proteomics. Nature, 2003, 422(6928), 233-237.
5. Gross, M.L.; Rempel, D.L. Fourier transform mass spectrometry. Science, 1984, 226(4672), 261-268.
6. Chernushevich, I.V.; Loboda, A.V.; Thomson, B.A. An introduction to quadrupole-time-of-flight mass spectrometry. J. Mass Spectrom., 2001, 36(8), 849-865.
7. Hop, C.; Bakhtiar, R. An Introduction to Electrospray Ionization and Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry: Essential Tools in a Modern Biotechnology Environment. Biospectroscopy, 1997, 3(4), 259-280. (Pubitemid 127782017)
8. Batoy, S.; Akhmetova, E.; Miladinovic, S.; Smeal, J.; Wilkins, C.L. Developments in MALDI Mass Spectrometry: The Quest for the Perfect Matrix. Appl. Spectrosc. Rev., 2008, 43, 485-550.
9. Bruins, A.P.; Covey, T.R.; Henion, J.D. Ion spray interface for combined liquid chromatography/atmospheric pressure ionization mass spectrometry. Anal. Chem., 1987, 59(22), 2642-2646. (Pubitemid 18530994)
10. Arpino, P. Combined liquid chromatography mass spectrometry. Part 111. Applications of thermospray. Mass Spectrom. Rev., 1992, 11, 3-40.
11. Roy, S.M.; Anderle, M.; Lin, H.; Becker, C.H. Differential expression profiling of serum proteins and metabolites for biomarker discovery. Int. J. Mass Spectrom., 2004, 238(2), 163-171.
12. Regnier, F.; Huang, G. Future potential of targeted component analysis by multidimensional liquid chromatography-mass spectrometry. J. Chromatogr. A, 1996, 750(1-2), 3-10. (Pubitemid 26374010)
13. Wu, S.L.; Amato, H.; Biringer, R.; Choudhary, G.; Shieh, P.; Hancock, W.S. Targeted proteomics of low-level proteins in human plasma by LC/MSn: using human growth hormone as a model system. J. Proteome Res., 2002, 1(5), 459-465.
14. Kislinger, T.; Cox, B.; Kannan, A.; Chung, C.; Hu, P.; Ignatchenko, A.; Scott, M.S.; Gramolini, A.O.; Morris, Q.; Hallett, M.T.; Rossant, J.; Hughes, T.R.; Frey, B.; Emili, A. Global Survey of Organ and Organelle Protein Expression in Mouse: Combined Proteomic and Transcriptomic Profiling. Cell, 2006, 125(1), 173-186.
15. Adkins, J.N.; Varnum, S.M.; Auberry, K.J.; Moore, R.J.; Angell, N.H.; Smith, R.D.; Springer, D.L.; Pounds, J.G. Toward a Human Blood Serum Proteome Analysis By Multidimensional Separation Coupled With Mass Spectrometry* S. Mol. Cell. Proteom., 2002, 1(12), 947-955.
16. Liu, H.; Sadygov, R.G.; Yates III, J.R. A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics. Nat. Biotechnol, 1999, 17, 994-999.
17. Valkenborg, D.; Assam, P.; Thomas, G.; Krols, L.; Kas, K.; Burzykowski, T. Using a Poisson approximation to predict the isotopic distribution of sulphur-containing peptides in a peptidecentric proteomic approach. Rapid Commun. Mass Spectrom., 2007, 21(20), 3387-3391. (Pubitemid 47598793)
18. Bayne, C.K.; Smith, D.H. A new method for estimating isotopic ratios from pulse-counting mass spectrometric data. Int. J. Mass Spectrom. Ion Process., 1984, 59(3), 315-323.
19. Senko, M.W.; Beu, S.C.; McLafferty, F.W. Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrom., 1995, 6(4), 229-233.
20. Rockwood, A.L.; Van Ordent, S.L.; Smith, R.D. Ultrahigh Resolution Isotope Distribution Calculations. Rapid Commun. Mass Spectrom., 1996, 10, 59.
21. Horn, D.M.; Zubarev, R.A.; McLafferty, F.W. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J. Am. Soc. Mass Spectrom., 2000, 11(4), 320-332.
22. Coombes, K.R.; Koomen, J.M.; Baggerly, K.A.; Morris, J.S.; Kobayashi, R. Understanding the characteristics of mass spectrometry data through the use of simulation. Cancer Inform., 2005, 1(1), 41-52.
23. Du, P.; Stolovitzky, G.; Horvatovich, P.; Bischoff, R.; Lim, J.; Suits, F. A noise model for mass spectrometry based proteomics. Bioinformatics, 2008, 24(8), 1070-1077.
24. Leptos, K.C.; Sarracino, D.A.; Jaffe, J.D.; Krastins, B.; Church, G.M. MapQuant: Open-source software for large-scale protein quantification. Proteomics, 2006, 6(6), 1770-1782.
25. Andreev, V.P.; Rejtar, T.; Chen, H.S.; Moskovets, E.V.; Ivanov, A.R.; Karger, B.L. A Universal Denoising and Peak Picking Algorithm for LC-MS Based on Matched Filtration in the Chromatographic Time Domain. Anal. Chem., 2003, 75(22), 6314-6326.
26. Gras, R.; Mueller, M.; Gasteiger, E.; Gay, S.; Binz, P.A.; Bienvenut, W.; Hoogland, C.; Sanchez, J.C.; Bairoch, A.; Hochstrasser, D.F. Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection. Electrophoresis, 1999, 20(18), 3535-3550.
27. Zhang, Z.; Guan, S.; Marshall, A.G. Enhancement of the effective resolution of mass spectra of high-mass biomolecules by maximum entropy-based deconvolution to eliminate the isotopic natural abundance distribution. J. Am. Soc. Mass Spectrom., 1997, 8(6), 659-670.
28. Monroe, M.E.; Tolic, N.; Jaitly, N.; Shaw, J.L.; Adkins, J.N.; Smith, R.D. VIPER: an advanced software package to support high-throughput LC-MS pep-tide identification. Bioinformatics, 2007, 23(15), 2021-2023.
29. Mueller, L.N.; Rinner, O.; Schmidt, A.; Letarte, S.; Bodenmiller, B.; Brusniak, M.Y.; Vitek, O.; Aebersold, R.; Muller, M. SuperHirn-a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics, 2007, 7(19), 3470-3480. (Pubitemid 47597670)
30. Sturm, M.; Bertsch, A.; Groepl, C.; Hildebrandt, A.; Hussong, R.; Lange, E.; Pfeifer, N.; Schulz-Trieglaff, O.; Zerck, A.; Reinert, K.; Kohlbacher, O. OpenMS-An open-source software framework for mass spectrometry. BMC Bioinformatics, 2008, 9(1), 163. (Pubitemid 351546699)
31. Li, X.; Yi, E.C.; Kemp, C.J.; Zhang, H.; Aebersold, R. A Software Suite for the Generation and Comparison of Peptide Arrays from Sets of Data Collected by Liquid Chromatography-Mass Spectrometry* S. Mol. Cell. Proteom., 2005, 4(9), 1328-1340. (Pubitemid 41448720)
32. Coifman, R.R.; Donoho, D.L. Translation invariant de-noising. Wavelets and Statistics. Springer Lecures Notes in Statistics, 1994, 103, 125-150.
33. Li, X.; Zhang, H.; Ranish, J.A.; Aebersold, R. Automated Statistical Analysis of Protein Abundance Ratios from Data Generated by Stable-Isotope Dilution and Tandem Mass Spectrometry. Anal. Chem., 2003, 75(23), 6648-6657. (Pubitemid 37493927)
34. Hastings, C.A.; Norton, S.M.; Roy, S. New algorithms for processing and peak detection in liquid chromatography/mass spectrometry data. Rapid Comm. Mass Spectrom., 2002, 16(5), 462-467. (Pubitemid 34174686)
35. Katajamaa, M.; Orešič, M. Processing methods for differential analysis of LC/MS profile data. BMC Bioinformatics, 2005, 6(1), 179. (Pubitemid 41372487)
36. Katajamaa, M.; Miettinen, J.; Oresic, M. MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics, 2006, 22(5), 634-636.
37. Du, P.; Sudha, R.; Prystowsky, M.B.; Angeletti, R.H. Data reduction of isotope-resolved LC-MS spectra. Bioinformatics, 2007, 23(11), 1394-1400.
38. Du, P.; Angeletti, R.H. Automatic deconvolution of isotope-resolved mass spectra using variable selection and quantized peptide mass distribution. Anal. Chem., 2006, 78(10), 3385-3392.
39. Hochstrasser, D.F.; Appel, R.D. Modeling peptide mass fingerprinting data using the atomic composition of peptides. Electrophoresis, 1999, 20, 3527-3534.
40. Bellew, M.; Coram, M.; Fitzgibbon, M.; Igra, M.; Randolph, T.; Wang, P.; May, D.; Eng, J.; Fang, R.; Lin, C.W.; Chen, J.; Goodlett, D.; Whiteaker, J.; Paulovich, A.; McIntosh, M. A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics, 2006, 22(15), 1902-1909. (Pubitemid 44283036)
41. Yu, W.; Wu, B.; Lin, N.; Stone, K.; Williams, K.; Zhao, H. Detecting and aligning peaks in mass spectrometry data with applications to MALDI. Comput. Biol. Chem., 2006, 30(1), 27-38.