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Volumn 14, Issue 2, 2015, Pages 1299-1307

Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in proteo wizard's msconvert

Author keywords

Continuous wavelet transformation; deisotoping; mass spectrometry; open source software; peak picking; precursor charge determination; signal deconvolution

Indexed keywords

ALGORITHM; ARTICLE; COMPARATIVE STUDY; COMPUTER PROGRAM; COMPUTER SIMULATION; HUMAN; MEASUREMENT ACCURACY; NOISE; NONHUMAN; PRECURSOR; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEOMICS; QUADRUPOLE MASS SPECTROMETRY; RADIOISOTOPE DISTRIBUTION; SIGNAL PROCESSING; TANDEM MASS SPECTROMETRY; WAVELET ANALYSIS; WAVELET BASED PEAK DETECTION; CHEMISTRY; PROCEDURES;

EID: 84922645016     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr500886y     Document Type: Article
Times cited : (42)

References (27)
  • 1
    • 84860464109 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics: Existing capabilities and future directions
    • Angel, T. E.; Aryal, U. K.; Hengel, S. M. Mass spectrometry-based proteomics: existing capabilities and future directions Chem. Soc. Rev. 2012, 41, 3912-28
    • (2012) Chem. Soc. Rev. , vol.41 , pp. 3912-3928
    • Angel, T.E.1    Aryal, U.K.2    Hengel, S.M.3
  • 2
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • Nesvizhskii, A. I.; Vitek, O.; Aebersold, R. Analysis and validation of proteomic data generated by tandem mass spectrometry Nat. Methods. 2007, 4, 787-797
    • (2007) Nat. Methods. , vol.4 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 3
    • 84865576726 scopus 로고    scopus 로고
    • Quantitative mass spectrometry in proteomics: Critical review update from 2007 to the present
    • Bantscheff, M.; Lemeer, S.; Savitski, M. M.; Kuster, B. Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present Anal. Bioanal. Chem. 2012, 404, 939-65
    • (2012) Anal. Bioanal. Chem. , vol.404 , pp. 939-965
    • Bantscheff, M.1    Lemeer, S.2    Savitski, M.M.3    Kuster, B.4
  • 4
    • 34147114217 scopus 로고    scopus 로고
    • LIMPIC: A computational method for the separation of protein MALDI-TOF-MS signals from noise
    • Mantini, D.; Petrucci, F.; Pieragostino, D. LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise BMC Bioinf. 2007, 8, 101
    • (2007) BMC Bioinf. , vol.8 , pp. 101
    • Mantini, D.1    Petrucci, F.2    Pieragostino, D.3
  • 5
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    • Cox, J.; Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Nat. Biotechnol. 2008, 26, 1367-72
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 6
    • 33747180294 scopus 로고    scopus 로고
    • A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
    • Bellew, M.; Coram, M.; Fitzgibbon, M. A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS Bioinformatics 2006, 22, 1902-9
    • (2006) Bioinformatics , vol.22 , pp. 1902-1909
    • Bellew, M.1    Coram, M.2    Fitzgibbon, M.3
  • 7
    • 42249108173 scopus 로고    scopus 로고
    • OpenMS-an open-source software framework for mass spectrometry
    • Sturm, M.; Bertsch, A.; Gröpl, C. OpenMS-an open-source software framework for mass spectrometry BMC Bioinf. 2008, 9, 163
    • (2008) BMC Bioinf. , vol.9 , pp. 163
    • Sturm, M.1    Bertsch, A.2    Gröpl, C.3
  • 8
    • 77956545745 scopus 로고    scopus 로고
    • A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data
    • Wang, P.; Yang, P.; Arthur, J.; Yang, J. Y. H. A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data Bioinformatics 2010, 26, 2242-9
    • (2010) Bioinformatics , vol.26 , pp. 2242-2249
    • Wang, P.1    Yang, P.2    Arthur, J.3    Yang, J.Y.H.4
  • 9
    • 33748659203 scopus 로고    scopus 로고
    • Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
    • Du, P.; Kibbe, W. A.; Lin, S. M. Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching Bioinformatics 2006, 22, 2059-2065
    • (2006) Bioinformatics , vol.22 , pp. 2059-2065
    • Du, P.1    Kibbe, W.A.2    Lin, S.M.3
  • 10
    • 34548136221 scopus 로고    scopus 로고
    • VIPER: An advanced software package to support high-throughput LC-MS peptide identification
    • Monroe, M. E.; Tolić, N.; Jaitly, N.; Shaw, J. L.; Adkins, J. N.; Smith, R. D. VIPER: an advanced software package to support high-throughput LC-MS peptide identification Bioinformatics 2007, 23, 2021-3
    • (2007) Bioinformatics , vol.23 , pp. 2021-2023
    • Monroe, M.E.1    Tolić, N.2    Jaitly, N.3    Shaw, J.L.4    Adkins, J.N.5    Smith, R.D.6
  • 11
    • 34547727671 scopus 로고    scopus 로고
    • High speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics datasets
    • Hoopmann, M. R.; Finney, G. L.; Maccoss, M. J. High speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics datasets Anal. Chem. 2007, 79, 5620-5632
    • (2007) Anal. Chem. , vol.79 , pp. 5620-5632
    • Hoopmann, M.R.1    Finney, G.L.2    MacCoss, M.J.3
  • 12
    • 0034582319 scopus 로고    scopus 로고
    • Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules
    • 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, 320-332
    • (2000) J. Am. Soc. Mass Spectrom. , vol.11 , pp. 320-332
    • Horn, D.M.1    Zubarev, R.A.2    McLafferty, F.W.3
  • 13
    • 0033456265 scopus 로고    scopus 로고
    • Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints Proteomics and 2-DE
    • Berndt, P.; Hobohm, U.; Langen, H.; Technologies, G.; Roche, F. H. Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints Proteomics and 2-DE Electrophoresis 1999, 20, 3521-3526
    • (1999) Electrophoresis , vol.20 , pp. 3521-3526
    • Berndt, P.1    Hobohm, U.2    Langen, H.3    Technologies, G.4    Roche, F.H.5
  • 14
    • 17344374730 scopus 로고    scopus 로고
    • Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection
    • Gras, R.; Müller, M.; Gasteiger, E. Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection Electrophoresis 1999, 20, 3535-3550
    • (1999) Electrophoresis , vol.20 , pp. 3535-3550
    • Gras, R.1    Müller, M.2    Gasteiger, E.3
  • 15
    • 58149209843 scopus 로고
    • Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions
    • 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, 229-233
    • (1995) J. Am. Soc. Mass Spectrom. , vol.6 , pp. 229-233
    • Senko, M.W.1    Beu, S.C.2    McLafferty, F.W.3
  • 16
    • 40249107822 scopus 로고    scopus 로고
    • Efficient analysis of mass spectrometry data using the isotope wavelet
    • Hussong, R.; Tholey, A.; Hildebrandt, A. Efficient analysis of mass spectrometry data using the isotope wavelet AIP Conf Proc. 2007, 940, 139-149
    • (2007) AIP Conf Proc. , vol.940 , pp. 139-149
    • Hussong, R.1    Tholey, A.2    Hildebrandt, A.3
  • 17
    • 33745238061 scopus 로고    scopus 로고
    • Determination of peptide and protein ion charge states by Fourier transformation of isotope-resolved mass spectra
    • Tabb, D. L.; Shah, M. B.; Strader, M. B.; Connelly, H. M.; Hettich, R. L.; Hurst, G. B. Determination of peptide and protein ion charge states by Fourier transformation of isotope-resolved mass spectra J. Am. Soc. Mass Spectrom. 2006, 17, 903-15
    • (2006) J. Am. Soc. Mass Spectrom. , vol.17 , pp. 903-915
    • Tabb, D.L.1    Shah, M.B.2    Strader, M.B.3    Connelly, H.M.4    Hettich, R.L.5    Hurst, G.B.6
  • 18
    • 0032010153 scopus 로고    scopus 로고
    • A universal algorithm for fast and automated charge state deconvolution of electrospray mass-to-charge ratio spectra
    • Zhang, Z.; Marshall, A. G. A universal algorithm for fast and automated charge state deconvolution of electrospray mass-to-charge ratio spectra J. Am. Soc. Mass Spectrom. 1998, 9, 225-33
    • (1998) J. Am. Soc. Mass Spectrom. , vol.9 , pp. 225-233
    • Zhang, Z.1    Marshall, A.G.2
  • 19
    • 84867345063 scopus 로고    scopus 로고
    • A cross-platform toolkit for mass spectrometry and proteomics
    • Chambers, M. C.; Maclean, B.; Burke, R. A cross-platform toolkit for mass spectrometry and proteomics Nat. Biotechnol. 2012, 30, 918-20
    • (2012) Nat. Biotechnol. , vol.30 , pp. 918-920
    • Chambers, M.C.1    MacLean, B.2    Burke, R.3
  • 20
    • 60549117342 scopus 로고    scopus 로고
    • Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis
    • Yang, C.; He, Z.; Yu, W. Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis BMC Bioinf. 2009, 10, 4
    • (2009) BMC Bioinf. , vol.10 , pp. 4
    • Yang, C.1    He, Z.2    Yu, W.3
  • 21
    • 65349138192 scopus 로고    scopus 로고
    • Benchmarking currently available SELDI-TOF MS preprocessing techniques
    • Emanuele, V. A.; Gurbaxani, B. M. Benchmarking currently available SELDI-TOF MS preprocessing techniques Proteomics 2009, 9, 1754-62
    • (2009) Proteomics , vol.9 , pp. 1754-1762
    • Emanuele, V.A.1    Gurbaxani, B.M.2
  • 22
    • 77955455399 scopus 로고    scopus 로고
    • Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies
    • Houel, S.; Abernathy, R.; Renganathan, K.; Meyer-arendt, K.; Ahn, N. G.; Old, W. M. Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies J. Proteome Res. 2010, 9, 4152-4160
    • (2010) J. Proteome Res. , vol.9 , pp. 4152-4160
    • Houel, S.1    Abernathy, R.2    Renganathan, K.3    Meyer-Arendt, K.4    Ahn, N.G.5    Old, W.M.6
  • 23
    • 55249118638 scopus 로고    scopus 로고
    • DirecTag: Accurate sequence tags from peptide MS/MS through statistical scoring
    • Tabb, D. L.; Ma, Z.; Martin, D. B.; Ham, A. L.; Chambers, M. C. DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring J. Proteome Res. 2008, 7, 3838-3846
    • (2008) J. Proteome Res. , vol.7 , pp. 3838-3846
    • Tabb, D.L.1    Ma, Z.2    Martin, D.B.3    Ham, A.L.4    Chambers, M.C.5
  • 24
    • 0033948589 scopus 로고    scopus 로고
    • Automatic Poisson peak harvesting for high throughput protein identification proteomics
    • Breen, E. J.; Hopwood, F. G.; Williams, K. L.; Wilkins, M. R. Automatic Poisson peak harvesting for high throughput protein identification proteomics Electrophoresis 2000, 21, 2243-2251
    • (2000) Electrophoresis , vol.21 , pp. 2243-2251
    • Breen, E.J.1    Hopwood, F.G.2    Williams, K.L.3    Wilkins, M.R.4
  • 25
    • 33847401893 scopus 로고    scopus 로고
    • MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
    • Tabb, D. L.; Fernando, C. G.; Chambers, M. C. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis J. Proteome Res. 2007, 6, 654-661
    • (2007) J. Proteome Res. , vol.6 , pp. 654-661
    • Tabb, D.L.1    Fernando, C.G.2    Chambers, M.C.3
  • 26
    • 50149117169 scopus 로고    scopus 로고
    • Spectral probabilities and generating functions of tandem mass spectra: A strike against decoy databases
    • Kim, S.; Gupta, N.; Pevzner, P. A. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases J. Proteome Res. 2008, 7, 3354-3363
    • (2008) J. Proteome Res. , vol.7 , pp. 3354-3363
    • Kim, S.1    Gupta, N.2    Pevzner, P.A.3
  • 27
    • 68549092907 scopus 로고    scopus 로고
    • IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering
    • Ma, Z.; Dasari, S.; Chambers, M. C. IDPicker 2.0: improved protein assembly with high discrimination peptide identification filtering J. Proteome Res. 2009, 8, 3872-3881
    • (2009) J. Proteome Res. , vol.8 , pp. 3872-3881
    • Ma, Z.1    Dasari, S.2    Chambers, M.C.3


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