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Volumn 12, Issue 2, 2012, Pages 226-235

pParse: A method for accurate determination of monoisotopic peaks in high-resolution mass spectra

Author keywords

Bioinformatics; Co eluted precursors; High resolution; Mass spectra; Monoisotopic peaks

Indexed keywords

CO ELUTED PRECURSOR; PEPTIDE; UNCLASSIFIED DRUG;

EID: 84862960055     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100081     Document Type: Article
Times cited : (59)

References (42)
  • 1
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R., Mann, M., Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 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
    • 0031623267 scopus 로고    scopus 로고
    • Fourier transform ion cyclotron resonance mass spectrometry: a primer
    • Marshall, A. G., Hendrickson, C. L., Jackson, G. S., Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom. Rev. 1998, 17, 1-35.
    • (1998) Mass Spectrom. Rev. , vol.17 , pp. 1-35
    • Marshall, A.G.1    Hendrickson, C.L.2    Jackson, G.S.3
  • 4
    • 18344364097 scopus 로고    scopus 로고
    • The Orbitrap: a new mass spectrometer
    • Hu, Q., Noll, R. J., Li, H., Makarov, A. et al., The Orbitrap: a new mass spectrometer. J. Mass Spectrom. 2005, 40, 430-443.
    • (2005) J. Mass Spectrom. , vol.40 , pp. 430-443
    • Hu, Q.1    Noll, R.J.2    Li, H.3    Makarov, A.4
  • 5
    • 0037314884 scopus 로고    scopus 로고
    • High mass measurement accuracy determination for proteomics using multivariate regression fitting: application to electrospray ionization time-of-flight mass spectrometry
    • Strittmatter, E. F., Rodriguez, N., Smith, R. D., High mass measurement accuracy determination for proteomics using multivariate regression fitting: application to electrospray ionization time-of-flight mass spectrometry. Anal. Chem. 2003, 75, 460-468.
    • (2003) Anal. Chem. , vol.75 , pp. 460-468
    • Strittmatter, E.F.1    Rodriguez, N.2    Smith, R.D.3
  • 6
    • 79953719716 scopus 로고    scopus 로고
    • More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS
    • Michalski, A., Cox, J., Mann, M., More than 100, 000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J. Proteome Res. 2011, 10, 1785-1793.
    • (2011) J. Proteome Res. , vol.10 , pp. 1785-1793
    • Michalski, A.1    Cox, J.2    Mann, M.3
  • 7
    • 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
  • 8
    • 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
  • 9
    • 62149121444 scopus 로고    scopus 로고
    • Decon2LS: an open-source software package for automated processing and visualization of high resolution mass spectrometry data
    • Jaitly, N., Mayampurath, A., Littlefield, K., Adkins, J. N. et al., Decon2LS: an open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics 2009, 10, 87.
    • (2009) BMC Bioinformatics , vol.10 , pp. 87
    • Jaitly, N.1    Mayampurath, A.2    Littlefield, K.3    Adkins, J.N.4
  • 10
    • 41349120246 scopus 로고    scopus 로고
    • DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra
    • Mayampurath, A. M., Jaitly, N., Purvine, S. O., Monroe, M. E. et al., DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics 2008, 24, 1021-1023.
    • (2008) Bioinformatics , vol.24 , pp. 1021-1023
    • Mayampurath, A.M.1    Jaitly, N.2    Purvine, S.O.3    Monroe, M.E.4
  • 11
    • 34547727671 scopus 로고    scopus 로고
    • High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry
    • Hoopmann, M. R., Finney, G. L., MacCoss, M. J., High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry. 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
    • 76149132007 scopus 로고    scopus 로고
    • Comparison of database search strategies for high precursor mass accuracy MS/MS data
    • Hsieh, E. J., Hoopmann, M. R., MacLean, B., MacCoss, M. J., Comparison of database search strategies for high precursor mass accuracy MS/MS data. J. Proteome Res. 2010, 9, 1138-1143.
    • (2010) J. Proteome Res. , vol.9 , pp. 1138-1143
    • Hsieh, E.J.1    Hoopmann, M.R.2    MacLean, B.3    MacCoss, M.J.4
  • 13
    • 73649131275 scopus 로고    scopus 로고
    • MSQuant, an open source platform for mass spectrometry-based quantitative proteomics
    • Mortensen, P., Gouw, J. W., Olsen, J. V., Ong, S. E. et al., MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J. Proteome Res. 2010, 9, 393-403.
    • (2010) J. Proteome Res. , vol.9 , pp. 393-403
    • Mortensen, P.1    Gouw, J.W.2    Olsen, J.V.3    Ong, S.E.4
  • 14
    • 20444495735 scopus 로고    scopus 로고
    • An automated method for the analysis of stable isotope labeling data in proteomics
    • Zhang, X., Hines, W., Adamec, J., Asara, J. M. et al., An automated method for the analysis of stable isotope labeling data in proteomics. J. Am. Soc. Mass Spectrom. 2005, 16, 1181-1191.
    • (2005) J. Am. Soc. Mass Spectrom. , vol.16 , pp. 1181-1191
    • Zhang, X.1    Hines, W.2    Adamec, J.3    Asara, J.M.4
  • 15
    • 54749148348 scopus 로고    scopus 로고
    • Isotopic peak intensity ratio based algorithm for determination of isotopic clusters and monoisotopic masses of polypeptides from high-resolution mass spectrometric data
    • Park, K., Yoon, J. Y., Lee, S., Paek, E. et al., Isotopic peak intensity ratio based algorithm for determination of isotopic clusters and monoisotopic masses of polypeptides from high-resolution mass spectrometric data. Anal. Chem. 2008, 80, 7294-7303.
    • (2008) Anal. Chem. , vol.80 , pp. 7294-7303
    • Park, K.1    Yoon, J.Y.2    Lee, S.3    Paek, E.4
  • 16
    • 27644514072 scopus 로고    scopus 로고
    • Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra
    • Zhang, J., Gao, W., Cai, J., He, S. et al., Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra. IEEE/ACM Trans. Comput. Biol. Bioinform. 2005, 2, 217-230.
    • (2005) IEEE/ACM Trans. Comput. Biol. Bioinform. , vol.2 , pp. 217-230
    • Zhang, J.1    Gao, W.2    Cai, J.3    He, S.4
  • 17
    • 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, 1367-1372.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 18
    • 29244448703 scopus 로고    scopus 로고
    • Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap
    • Olsen, J. V., de Godoy, L. M., Li, G., Macek, B. et al., Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteomics 2005, 4, 2010-2021.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 2010-2021
    • Olsen, J.V.1    de Godoy, L.M.2    Li, G.3    Macek, B.4
  • 19
    • 34548136221 scopus 로고    scopus 로고
    • VIPER: an advanced software package to support high-throughput LC-MS peptide identification
    • Monroe, M. E., Tolic, N., Jaitly, N., Shaw, J. L. et al., VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics 2007, 23, 2021-2023.
    • (2007) Bioinformatics , vol.23 , pp. 2021-2023
    • Monroe, M.E.1    Tolic, N.2    Jaitly, N.3    Shaw, J.L.4
  • 20
    • 35348965139 scopus 로고    scopus 로고
    • SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling
    • Mueller, L. N., Rinner, O., Schmidt, A., Letarte, S. et al., SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 2007, 7, 3470-3480.
    • (2007) Proteomics , vol.7 , pp. 3470-3480
    • Mueller, L.N.1    Rinner, O.2    Schmidt, A.3    Letarte, S.4
  • 21
    • 33645463331 scopus 로고    scopus 로고
    • MapQuant: open-source software for large-scale protein quantification
    • 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, 1770-1782.
    • (2006) Proteomics , vol.6 , pp. 1770-1782
    • Leptos, K.C.1    Sarracino, D.A.2    Jaffe, J.D.3    Krastins, B.4    Church, G.M.5
  • 22
    • 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., Igra, M. et al., A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 2006, 22, 1902-1909.
    • (2006) Bioinformatics , vol.22 , pp. 1902-1909
    • Bellew, M.1    Coram, M.2    Fitzgibbon, M.3    Igra, M.4
  • 23
    • 26844492976 scopus 로고    scopus 로고
    • A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry
    • Li, X. J., 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. Mol. Cell. Proteomics 2005, 4, 1328-1340.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1328-1340
    • Li, X.J.1    Yi, E.C.2    Kemp, C.J.3    Zhang, H.4    Aebersold, R.5
  • 24
    • 33644867564 scopus 로고    scopus 로고
    • MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data
    • Katajamaa, M., Miettinen, J., Oresic, M., MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 2006, 22, 634-636.
    • (2006) Bioinformatics , vol.22 , pp. 634-636
    • Katajamaa, M.1    Miettinen, J.2    Oresic, M.3
  • 25
    • 70549106483 scopus 로고    scopus 로고
    • Review of peak detection algorithms in liquid-chromatography-mass spectrometry
    • Zhang, J., Gonzalez, E., Hestilow, T., Haskins, W., Huang, Y., Review of peak detection algorithms in liquid-chromatography-mass spectrometry. Curr. Genomics 2009, 10, 388-401.
    • (2009) Curr. Genomics , vol.10 , pp. 388-401
    • Zhang, J.1    Gonzalez, E.2    Hestilow, T.3    Haskins, W.4    Huang, Y.5
  • 26
    • 48949099046 scopus 로고    scopus 로고
    • Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses
    • Scherl, A., Tsai, Y. S., Shaffer, S. A., Goodlett, D. R., Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses. Proteomics 2008, 8, 2791-2797.
    • (2008) Proteomics , vol.8 , pp. 2791-2797
    • Scherl, A.1    Tsai, Y.S.2    Shaffer, S.A.3    Goodlett, D.R.4
  • 27
    • 55249111329 scopus 로고    scopus 로고
    • Precursor-ion mass re-estimation improves peptide identification on hybrid instruments
    • Luethy, R., Kessner, D. E., Katz, J. E., Maclean, B. et al., Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. J. Proteome Res. 2008, 7, 4031-4039.
    • (2008) J. Proteome Res. , vol.7 , pp. 4031-4039
    • Luethy, R.1    Kessner, D.E.2    Katz, J.E.3    Maclean, B.4
  • 28
    • 70350018231 scopus 로고    scopus 로고
    • YADA: a tool for taking the most out of high-resolution spectra
    • Carvalho, P. C., Xu, T., Han, X., Cociorva, D. et al., YADA: a tool for taking the most out of high-resolution spectra. Bioinformatics 2009, 25, 2734-2736.
    • (2009) Bioinformatics , vol.25 , pp. 2734-2736
    • Carvalho, P.C.1    Xu, T.2    Han, X.3    Cociorva, D.4
  • 29
    • 27744469683 scopus 로고    scopus 로고
    • ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer
    • Zhang, N., Li, X. J., Ye, M., Pan, S. et al., ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer. Proteomics 2005, 5, 4096-4106.
    • (2005) Proteomics , vol.5 , pp. 4096-4106
    • Zhang, N.1    Li, X.J.2    Ye, M.3    Pan, S.4
  • 30
    • 79953701087 scopus 로고    scopus 로고
    • Andromeda: a peptide search engine integrated into the MaxQuant environment
    • Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A. et al., Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 2011, 10, 1794-1805.
    • (2011) J. Proteome Res. , vol.10 , pp. 1794-1805
    • Cox, J.1    Neuhauser, N.2    Michalski, A.3    Scheltema, R.A.4
  • 31
    • 83055182134 scopus 로고    scopus 로고
    • Peptide identification by database search of mixture tandem mass spectra
    • M111.010017.
    • Wang, J., Bourne, P. E., Bandeira, N., Peptide identification by database search of mixture tandem mass spectra. Mol. Cell. Proteomics 2011, 10, M111.010017.
    • (2011) Mol. Cell. Proteomics , vol.10
    • Wang, J.1    Bourne, P.E.2    Bandeira, N.3
  • 32
    • 48249100480 scopus 로고    scopus 로고
    • Detection of co-eluted peptides using database search methods
    • Alves, G., Ogurtsov, A. Y., Kwok, S., Wu, W. W. et al., Detection of co-eluted peptides using database search methods. Biol. Direct 2008, 3, 27.
    • (2008) Biol. Direct , vol.3 , pp. 27
    • Alves, G.1    Ogurtsov, A.Y.2    Kwok, S.3    Wu, W.W.4
  • 33
    • 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. et al., 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
  • 35
    • 71049143452 scopus 로고    scopus 로고
    • Unique ion signature mass spectrometry, a deterministic method to assign peptide identity
    • Sherman, J., McKay, M. J., Ashman, K., Molloy, M. P., Unique ion signature mass spectrometry, a deterministic method to assign peptide identity. Mol. Cell. Proteomics 2009, 8, 2051-2062.
    • (2009) Mol. Cell. Proteomics , vol.8 , pp. 2051-2062
    • Sherman, J.1    McKay, M.J.2    Ashman, K.3    Molloy, M.P.4
  • 36
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database
    • Eng, J. K., Mccormack, A. L., Yates, J. R., An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , pp. 976-989
    • Eng, J.K.1    Mccormack, A.L.2    Yates, J.R.3
  • 37
    • 4444237022 scopus 로고    scopus 로고
    • Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry
    • Fu, Y., Yang, Q., Sun, R., Li, D. et al., Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry. Bioinformatics 2004, 20, 1948-1954.
    • (2004) Bioinformatics , vol.20 , pp. 1948-1954
    • Fu, Y.1    Yang, Q.2    Sun, R.3    Li, D.4
  • 38
    • 34548620571 scopus 로고    scopus 로고
    • pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry
    • Wang, L. H., Li, D. Q., Fu, Y., Wang, H. P. et al., pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry. Rapid Commun. Mass Spectrom. 2007, 21, 2985-2991.
    • (2007) Rapid Commun. Mass Spectrom. , vol.21 , pp. 2985-2991
    • Wang, L.H.1    Li, D.Q.2    Fu, Y.3    Wang, H.P.4
  • 39
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D. N., Pappin, D. J., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 40
    • 24044513966 scopus 로고    scopus 로고
    • Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations
    • Elias, J. E., Haas, W., Faherty, B. K., Gygi, S. P., Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2005, 2, 667-675.
    • (2005) Nat. Methods , vol.2 , pp. 667-675
    • Elias, J.E.1    Haas, W.2    Faherty, B.K.3    Gygi, S.P.4
  • 41
    • 55249118638 scopus 로고    scopus 로고
    • DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring
    • Tabb, D. L., Ma, Z.-Q., Martin, D. B., Ham, A.-J. 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.-Q.2    Martin, D.B.3    Ham, A.-J.L.4    Chambers, M.C.5
  • 42
    • 34547572949 scopus 로고    scopus 로고
    • Is proteomics the new genomics?
    • Cox, J., Mann, M., Is proteomics the new genomics? Cell 2007, 130, 395-398.
    • (2007) Cell , vol.130 , pp. 395-398
    • Cox, J.1    Mann, M.2


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