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Volumn 31, Issue 4, 2015, Pages 555-562

DIANA-algorithmic improvements for analysis of data-independent acquisition MS data

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PEPTIDE FRAGMENT;

EID: 84928999619     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu686     Document Type: Article
Times cited : (85)

References (39)
  • 1
    • 84898715794 scopus 로고    scopus 로고
    • Intelligent data acquisition blends targeted and discovery methods
    • Bailey, D.J. et al. (2014) Intelligent data acquisition blends targeted and discovery methods. J. Proteome Res., 13, 2152-2161.
    • (2014) J. Proteome Res. , vol.13 , pp. 2152-2161
    • Bailey, D.J.1
  • 3
    • 27144468026 scopus 로고    scopus 로고
    • The global burden of group A streptococcal diseases
    • Carapetis, J.R. et al. (2005) The global burden of group A streptococcal diseases. Lancet Infect. Dis., 5, 685-694.
    • (2005) Lancet Infect. Dis. , vol.5 , pp. 685-694
    • Carapetis, J.R.1
  • 4
    • 84867345063 scopus 로고    scopus 로고
    • A cross-platform toolkit for mass spectrometry and proteomics
    • Chambers, M.C. et al. (2012) A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol., 30, 918-920.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 918-920
    • Chambers, M.C.1
  • 5
    • 84888858053 scopus 로고    scopus 로고
    • Quantifying protein interaction dynamics by SWATH mass spectrometry: Application to the 14-3-3 system
    • Collins, B.C. et al. (2013) Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat. Methods, 10, 1246-1253.
    • (2013) Nat. Methods , vol.10 , pp. 1246-1253
    • Collins, B.C.1
  • 6
    • 33644876912 scopus 로고    scopus 로고
    • The PeptideAtlas project
    • Desiere, F. et al. (2006) The PeptideAtlas project. Nucleic Acids Res., 34, D655-658.
    • (2006) Nucleic Acids Res. , vol.34 , pp. D655-658
    • Desiere, F.1
  • 7
    • 84859843750 scopus 로고    scopus 로고
    • TraML - A standard format for exchange of selected reaction monitoring transition lists
    • R111.015040
    • Deutsch, E.W. et al. (2012) TraML-a standard format for exchange of selected reaction monitoring transition lists. Mol. Cell. Proteomics, 11, R111.015040.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Deutsch, E.W.1
  • 8
    • 84881477986 scopus 로고    scopus 로고
    • Multiplexed MS/MS for improved data-independent acquisition
    • Egertson, J.D. et al. (2013) Multiplexed MS/MS for improved data-independent acquisition. Nat. Methods, 10, 744-746.
    • (2013) Nat. Methods , vol.10 , pp. 744-746
    • Egertson, J.D.1
  • 9
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias, J.E. and Gygi, S.P. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods, 4, 207-214.
    • (2007) Nat. Methods , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 10
    • 84860869167 scopus 로고    scopus 로고
    • Using iRT, a normalized retention time for more targeted measurement of peptides
    • Escher, C. et al. (2012) Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics, 12, 1111-1121.
    • (2012) Proteomics , vol.12 , pp. 1111-1121
    • Escher, C.1
  • 11
    • 84860856503 scopus 로고    scopus 로고
    • PASSEL: The PeptideAtlas SRMexperiment library
    • Farrah, T. et al. (2012) PASSEL: the PeptideAtlas SRMexperiment library. Proteomics, 12, 1170-1175.
    • (2012) Proteomics , vol.12 , pp. 1170-1175
    • Farrah, T.1
  • 12
    • 84861860481 scopus 로고    scopus 로고
    • Targeted data extraction of the MS/MS spectra generated by data independent acquisition: A new concept for consistent and accurate proteome analysis
    • O111.016717
    • Gillet, L.C. et al. (2012) Targeted data extraction of the MS/MS spectra generated by data independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics, 11, O111.016717.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Gillet, L.C.1
  • 13
    • 67049100049 scopus 로고    scopus 로고
    • The proteios software environment: An extensible multiuser platform for management and analysis of proteomics data
    • Hakkinen, J. et al. (2009) The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data. J. Proteome Res., 8, 3037-3043.
    • (2009) J. Proteome Res. , vol.8 , pp. 3037-3043
    • Hakkinen, J.1
  • 14
    • 63049120021 scopus 로고    scopus 로고
    • Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
    • Jones, A.R. et al. (2009) Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. Proteomics, 9, 1220-1229.
    • (2009) Proteomics , vol.9 , pp. 1220-1229
    • Jones, A.R.1
  • 15
    • 38649083118 scopus 로고    scopus 로고
    • Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
    • Kall, L. et al. (2008) Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J. Proteome Res., 7, 29-34.
    • (2008) J. Proteome Res. , vol.7 , pp. 29-34
    • Kall, L.1
  • 16
    • 84871791617 scopus 로고    scopus 로고
    • Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes
    • Karlsson, C. et al. (2012) Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. Nat. Commun., 3, 1301.
    • (2012) Nat. Commun. , vol.3 , pp. 1301
    • Karlsson, C.1
  • 18
    • 3242731195 scopus 로고    scopus 로고
    • A model for random sampling and estimation of relative protein abundance in shotgun proteomics
    • Liu, H. et al. (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem., 76, 4193-4201.
    • (2004) Anal. Chem. , vol.76 , pp. 4193-4201
    • Liu, H.1
  • 19
    • 84855510493 scopus 로고    scopus 로고
    • Streptococcus pyogenes in human plasma: Adaptive mechanisms analyzed by mass spectrometry-based proteomics
    • Malmstrom, J. et al. (2012) Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry-based proteomics. J. Biol. Chem., 287, 1415-1425.
    • (2012) J. Biol. Chem. , vol.287 , pp. 1415-1425
    • Malmstrom, J.1
  • 20
    • 78651082595 scopus 로고    scopus 로고
    • MzML - A community standard for mass spectrometry data
    • R110.000133
    • Martens, L. et al. (2011) mzML-a community standard for mass spectrometry data. Mol. Cell. Proteomics, 10, R110.000133.
    • (2011) Mol. Cell. Proteomics , vol.10
    • Martens, L.1
  • 21
    • 79961225176 scopus 로고    scopus 로고
    • Probabilistic consensus scoring improves tandem mass spectrometry peptide identification
    • Nahnsen, S. et al. (2011) Probabilistic consensus scoring improves tandem mass spectrometry peptide identification. J. Proteome Res., 10, 3332-3343.
    • (2011) J. Proteome Res. , vol.10 , pp. 3332-3343
    • Nahnsen, S.1
  • 22
    • 68049114653 scopus 로고    scopus 로고
    • Precursor acquisition independent from ion count: How to dive deeper into the proteomics ocean
    • Panchaud, A. et al. (2009) Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal. Chem., 81, 6481-6488.
    • (2009) Anal. Chem. , vol.81 , pp. 6481-6488
    • Panchaud, A.1
  • 23
    • 80555140075 scopus 로고    scopus 로고
    • Scikit-learn: Machine learning in Python
    • Pedregosa, F. et al. (2011) Scikit-learn: machine learning in Python. J. Mach. Learn. Res., 12, 2825-2830.
    • (2011) J. Mach. Learn. Res. , vol.12 , pp. 2825-2830
    • Pedregosa, F.1
  • 24
    • 54049095667 scopus 로고    scopus 로고
    • A database of mass spectrometric assays for the yeast prote-ome
    • Picotti, P. et al. (2008) A database of mass spectrometric assays for the yeast prote-ome. Nat. Methods, 5, 913-914.
    • (2008) Nat. Methods , vol.5 , pp. 913-914
    • Picotti, P.1
  • 25
    • 68749094119 scopus 로고    scopus 로고
    • Full dynamic range proteome analysis of S. Cerevisiae by targeted proteomics
    • Picotti, P. et al. (2009) Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell, 138, 795-806.
    • (2009) Cell , vol.138 , pp. 795-806
    • Picotti, P.1
  • 26
    • 33745777632 scopus 로고    scopus 로고
    • UPLC/MS(E); A new approach for generating molecular fragment information for biomarker structure elucidation
    • Plumb, R.S. et al. (2006) UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid Commun. Mass Spectrom., 20, 1989-1994.
    • (2006) Rapid Commun. Mass Spectrom. , vol.20 , pp. 1989-1994
    • Plumb, R.S.1
  • 27
    • 0038047154 scopus 로고    scopus 로고
    • Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer
    • Purvine, S. et al. (2003) Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics, 3, 847-850.
    • (2003) Proteomics , vol.3 , pp. 847-850
    • Purvine, S.1
  • 28
    • 79955595074 scopus 로고    scopus 로고
    • MProphet: Automated data processing and statistical validation for large-scale SRM experiments
    • Reiter, L. et al. (2011) mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat. Methods, 8, 430-435.
    • (2011) Nat. Methods , vol.8 , pp. 430-435
    • Reiter, L.1
  • 29
    • 84898665956 scopus 로고    scopus 로고
    • OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data
    • Rost, H.L. et al. (2014) OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat. Biotechnol., 32, 219-223.
    • (2014) Nat. Biotechnol. , vol.32 , pp. 219-223
    • Rost, H.L.1
  • 30
    • 80053387432 scopus 로고    scopus 로고
    • IProphet: Multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
    • M111.007690
    • Shteynberg, D. et al. (2011) iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol. Cell. Proteomics, 10, M111.007690.
    • (2011) Mol. Cell. Proteomics , vol.10
    • Shteynberg, D.1
  • 31
    • 84884363278 scopus 로고    scopus 로고
    • Combining results of multiple search engines in prote-omics
    • Shteynberg, D. et al. (2013) Combining results of multiple search engines in prote-omics. Mol. Cell. Proteomics, 12, 2383-2393.
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 2383-2393
    • Shteynberg, D.1
  • 33
    • 76149142168 scopus 로고    scopus 로고
    • Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry
    • Tabb, D.L. et al. (2010) Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J. Proteome Res., 9, 761-776.
    • (2010) J. Proteome Res. , vol.9 , pp. 761-776
    • Tabb, D.L.1
  • 34
    • 84863624355 scopus 로고    scopus 로고
    • Automated selected reaction monitoring software for accurate label-free protein quantification
    • Teleman, J. et al. (2012) Automated selected reaction monitoring software for accurate label-free protein quantification. J. Proteome Res., 11, 3766-3773.
    • (2012) J. Proteome Res. , vol.11 , pp. 3766-3773
    • Teleman, J.1
  • 35
    • 84901931503 scopus 로고    scopus 로고
    • Numerical compression schemes for proteomics mass spec-trometry data
    • Teleman, J. et al. (2014) Numerical compression schemes for proteomics mass spec-trometry data. Mol. Cell. Proteomics, 13, 1537-1542.
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 1537-1542
    • Teleman, J.1
  • 36
    • 84874630267 scopus 로고    scopus 로고
    • Segmentation of precursor mass range using 'tiling' approach increases peptide identifications for MS1-based label-free quantification
    • Vincent, C.E. et al. (2013) Segmentation of precursor mass range using 'tiling' approach increases peptide identifications for MS1-based label-free quantification. Anal. Chem., 85, 2825-2832.
    • (2013) Anal. Chem. , vol.85 , pp. 2825-2832
    • Vincent, C.E.1
  • 37
    • 84860603290 scopus 로고    scopus 로고
    • Protein expression changes in ovarian cancer during the transition from benign to malignant
    • Waldemarson, S. et al. (2012) Protein expression changes in ovarian cancer during the transition from benign to malignant. J. Proteome Res., 11, 2876-2889.
    • (2012) J. Proteome Res. , vol.11 , pp. 2876-2889
    • Waldemarson, S.1
  • 38
    • 84857811076 scopus 로고    scopus 로고
    • Accuratepeptidefragmentmassanalysis:multiplexed pep-tide identification and quantification
    • Weisbrod, C.R. et al. (2012)Accuratepeptidefragmentmassanalysis:multiplexed pep-tide identification and quantification. J. Proteome Res., 11, 1621-1632.
    • (2012) J. Proteome Res. , vol.11 , pp. 1621-1632
    • Weisbrod, C.R.1
  • 39
    • 34250722602 scopus 로고    scopus 로고
    • Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks
    • Wolf-Yadlin, A. et al. (2007) Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc. Natl Acad. Sci. USA, 104, 5860-5865.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 5860-5865
    • Wolf-Yadlin, A.1


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