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Volumn 14, Issue 10, 2015, Pages 4359-4371

The Use of Variable Q1 Isolation Windows Improves Selectivity in LC-SWATH-MS Acquisition

Author keywords

metabolomics; proteomics; selectivity; SWATH; variable Q1 window widths

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA PROCESSING; DENDRITIC CELL; HUMAN; HUMAN CELL; ION CURRENT; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLOMICS; PRIORITY JOURNAL; PROTEOMICS; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; SENSITIVITY ANALYSIS; AMINO ACID SEQUENCE; CHEMISTRY; DEVICES; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; PRIMARY CELL CULTURE; PROCEDURES; PROTEIN DEGRADATION; REVERSED PHASE LIQUID CHROMATOGRAPHY; TANDEM MASS SPECTROMETRY; URINE;

EID: 84942944020     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00543     Document Type: Article
Times cited : (151)

References (29)
  • 1
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn, M. P.; Wolters, D.; Yates, J. R., 3rd Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nat. Biotechnol. 2001, 19, 242-247 10.1038/85686
    • (2001) Nat. Biotechnol. , vol.19 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates, J.R.3
  • 2
    • 0037277179 scopus 로고    scopus 로고
    • Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome
    • Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome J. Proteome Res. 2003, 2, 43-50 10.1021/pr025556v
    • (2003) J. Proteome Res. , vol.2 , pp. 43-50
    • Peng, J.1    Elias, J.E.2    Thoreen, C.C.3    Licklider, L.J.4    Gygi, S.P.5
  • 3
    • 33749990257 scopus 로고    scopus 로고
    • Proteome profile of the MCF7 cancer cell line: A mass spectrometric evaluation
    • Sarvaiya, H. A.; Yoon, J. H.; Lazar, I. M. Proteome profile of the MCF7 cancer cell line: a mass spectrometric evaluation Rapid Commun. Mass Spectrom. 2006, 20, 3039-3055 10.1002/rcm.2677
    • (2006) Rapid Commun. Mass Spectrom. , vol.20 , pp. 3039-3055
    • Sarvaiya, H.A.1    Yoon, J.H.2    Lazar, I.M.3
  • 4
    • 84876806581 scopus 로고    scopus 로고
    • Mass Spectrometry-based Quantitative Proteomic Profiling of Human Pancreatic and Hepatic Stellate Cell Lines
    • Paulo, J. A.; Kadiyala, V.; Banks, P. A.; Conwell, D. L.; Steen, H. Mass Spectrometry-based Quantitative Proteomic Profiling of Human Pancreatic and Hepatic Stellate Cell Lines Genomics, Proteomics Bioinf. 2013, 11, 105-113 10.1016/j.gpb.2013.01.009
    • (2013) Genomics, Proteomics Bioinf. , vol.11 , pp. 105-113
    • Paulo, J.A.1    Kadiyala, V.2    Banks, P.A.3    Conwell, D.L.4    Steen, H.5
  • 5
    • 84906075221 scopus 로고    scopus 로고
    • Deep proteomic profiling of human carotid atherosclerotic plaques using multidimensional LC-MS/MS
    • Hao, P.; Ren, Y.; Pasterkamp, G.; Moll, F. L.; de Kleijn, D. P.; Sze, S. K. Deep proteomic profiling of human carotid atherosclerotic plaques using multidimensional LC-MS/MS Proteomics: Clin. Appl. 2014, 8, 631-635 10.1002/prca.201400007
    • (2014) Proteomics: Clin. Appl. , vol.8 , pp. 631-635
    • Hao, P.1    Ren, Y.2    Pasterkamp, G.3    Moll, F.L.4    De Kleijn, D.P.5    Sze, S.K.6
  • 6
    • 84870913642 scopus 로고    scopus 로고
    • Metabolomics Analysis of the Responses to Partial Hepatectomy in Hepatocellular Carcinoma Patients
    • Chan, W. Metabolomics Analysis of the Responses to Partial Hepatectomy in Hepatocellular Carcinoma Patients Am. J. Anal. Chem. 2011, 2, 142-151 10.4236/ajac.2011.22016
    • (2011) Am. J. Anal. Chem. , vol.2 , pp. 142-151
    • Chan, W.1
  • 7
    • 80053917679 scopus 로고    scopus 로고
    • Characterization of the human tear metabolome by LC-MS/MS
    • Chen, L.; Zhou, L.; Chan, E. C.; Neo, J.; Beuerman, R. W. Characterization of the human tear metabolome by LC-MS/MS J. Proteome Res. 2011, 10, 4876-4882 10.1021/pr2004874
    • (2011) J. Proteome Res. , vol.10 , pp. 4876-4882
    • Chen, L.1    Zhou, L.2    Chan, E.C.3    Neo, J.4    Beuerman, R.W.5
  • 9
    • 3242731195 scopus 로고    scopus 로고
    • A model for random sampling and estimation of relative protein abundance in shotgun proteomics
    • Liu, H.; Sadygov, R. G.; Yates, J. R., 3rd A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal. Chem. 2004, 76, 4193-4201 10.1021/ac0498563
    • (2004) Anal. Chem. , vol.76 , pp. 4193-4201
    • Liu, H.1    Sadygov, R.G.2    Yates, J.R.3
  • 11
  • 12
    • 14744293536 scopus 로고    scopus 로고
    • Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra
    • Venable, J. D.; Dong, M. Q.; Wohlschlegel, J.; Dillin, A.; Yates, J. R. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra Nat. Methods 2004, 1, 39-45 10.1038/nmeth705
    • (2004) Nat. Methods , vol.1 , pp. 39-45
    • Venable, J.D.1    Dong, M.Q.2    Wohlschlegel, J.3    Dillin, A.4    Yates, J.R.5
  • 13
    • 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
    • Gillet, L. C.; Navarro, P.; Tate, S.; Rost, H.; Selevsek, N.; Reiter, L.; Bonner, R.; Aebersold, R. 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 2012, 11, O111.016717 10.1074/mcp.O111.016717
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. O111016717
    • Gillet, L.C.1    Navarro, P.2    Tate, S.3    Rost, H.4    Selevsek, N.5    Reiter, L.6    Bonner, R.7    Aebersold, R.8
  • 14
    • 84923163979 scopus 로고    scopus 로고
    • The beauty of being (label)-free: Sample preparation methods for SWATH-MS and next-generation targeted proteomics
    • Vowinckel, J.; Capuano, F.; Campbell, K.; Deery, M. J.; Lilley, K. S.; Ralser, M. The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics F1000Research 2014, 2:272, 1-26 10.12688/f1000research.2-272.v2
    • (2014) F1000Research , vol.2272 , pp. 1-26
    • Vowinckel, J.1    Capuano, F.2    Campbell, K.3    Deery, M.J.4    Lilley, K.S.5    Ralser, M.6
  • 15
    • 84859107186 scopus 로고    scopus 로고
    • High-resolution mass spectrometry for integrated qualitative and quantitative analysis of pharmaceuticals in biological matrices
    • Hopfgartner, G.; Tonoli, D.; Varesio, E. High-resolution mass spectrometry for integrated qualitative and quantitative analysis of pharmaceuticals in biological matrices Anal. Bioanal. Chem. 2012, 402, 2587-2596 10.1007/s00216-011-5641-8
    • (2012) Anal. Bioanal. Chem. , vol.402 , pp. 2587-2596
    • Hopfgartner, G.1    Tonoli, D.2    Varesio, E.3
  • 16
    • 84892759900 scopus 로고    scopus 로고
    • Comparison of Information-Dependent Acquisition, SWATH, and MSAll Techniques in Metabolite Identification Study Employing Ultrahigh-Performance Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry
    • Zhu, X.; Chen, Y.; Subramanian, R. Comparison of Information-Dependent Acquisition, SWATH, and MSAll Techniques in Metabolite Identification Study Employing Ultrahigh-Performance Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry Anal. Chem. 2014, 86, 1202-1209 10.1021/ac403385y
    • (2014) Anal. Chem. , vol.86 , pp. 1202-1209
    • Zhu, X.1    Chen, Y.2    Subramanian, R.3
  • 17
    • 84898732425 scopus 로고    scopus 로고
    • Quantitative proteomics by SWATH-MS reveals altered expression of nucleic acid binding and regulatory proteins in HIV-1-infected macrophages
    • Haverland, N. A.; Fox, H. S.; Ciborowski, P. Quantitative proteomics by SWATH-MS reveals altered expression of nucleic acid binding and regulatory proteins in HIV-1-infected macrophages J. Proteome Res. 2014, 13, 2109-2119 10.1021/pr4012602
    • (2014) J. Proteome Res. , vol.13 , pp. 2109-2119
    • Haverland, N.A.1    Fox, H.S.2    Ciborowski, P.3
  • 19
    • 84888858053 scopus 로고    scopus 로고
    • Quantifying protein interaction dynamics by SWATH mass spectrometry: Application to the 14-3-3 system
    • Collins, B. C.; Gillet, L. C.; Rosenberger, G.; Rost, H. L.; Vichalkovski, A.; Gstaiger, M.; Aebersold, R. Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system Nat. Methods 2013, 10, 1246-1253 10.1038/nmeth.2703
    • (2013) Nat. Methods , vol.10 , pp. 1246-1253
    • Collins, B.C.1    Gillet, L.C.2    Rosenberger, G.3    Rost, H.L.4    Vichalkovski, A.5    Gstaiger, M.6    Aebersold, R.7
  • 20
    • 84935899784 scopus 로고    scopus 로고
    • Optimization of human dendritic cell sample preparation for mass spectrometry-based proteomics studies
    • Zhang, Y.; Bottinelli, D.; Lisacek, F.; Luban, J.; De Castillia, C. S.; Varesio, E.; Hopfgartner, G. Optimization of human dendritic cell sample preparation for mass spectrometry-based proteomics studies Anal. Biochem. 2015, 484, 40 10.1016/j.ab.2015.05.007
    • (2015) Anal. Biochem. , vol.484 , pp. 40
    • Zhang, Y.1    Bottinelli, D.2    Lisacek, F.3    Luban, J.4    De Castillia, C.S.5    Varesio, E.6    Hopfgartner, G.7
  • 21
    • 34848889259 scopus 로고    scopus 로고
    • The Paragon Algorithm, a Next Generation Search Engine That Uses Sequence Temperature Values and Feature Probabilities to Identify Peptides from Tandem Mass Spectra
    • Shilov, I. V.; Seymour, S. L.; Patel, A. A.; Loboda, A.; Tang, W. H.; Keating, S. P.; Hunter, C. L.; Nuwaysir, L. M.; Schaeffer, D. A. The Paragon Algorithm, a Next Generation Search Engine That Uses Sequence Temperature Values and Feature Probabilities to Identify Peptides from Tandem Mass Spectra Mol. Cell. Proteomics 2007, 6, 1638-1655 10.1074/mcp.T600050-MCP200
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 1638-1655
    • Shilov, I.V.1    Seymour, S.L.2    Patel, A.A.3    Loboda, A.4    Tang, W.H.5    Keating, S.P.6    Hunter, C.L.7    Nuwaysir, L.M.8    Schaeffer, D.A.9
  • 23
    • 55249121202 scopus 로고    scopus 로고
    • Nonlinear Fitting Method for Determining Local False Discovery Rates from Decoy Database Searches
    • Tang, W. H.; Shilov, I. V.; Seymour, S. L. Nonlinear Fitting Method for Determining Local False Discovery Rates from Decoy Database Searches J. Proteome Res. 2008, 7, 3661-3667 10.1021/pr070492f
    • (2008) J. Proteome Res. , vol.7 , pp. 3661-3667
    • Tang, W.H.1    Shilov, I.V.2    Seymour, S.L.3
  • 26
    • 84904094826 scopus 로고    scopus 로고
    • Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics
    • Toprak, U. H.; Gillet, L. C.; Maiolica, A.; Navarro, P.; Leitner, A.; Aebersold, R. Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics Mol. Cell. Proteomics 2014, 13, 2056-2071 10.1074/mcp.O113.036475
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 2056-2071
    • Toprak, U.H.1    Gillet, L.C.2    Maiolica, A.3    Navarro, P.4    Leitner, A.5    Aebersold, R.6
  • 28
    • 79951901773 scopus 로고    scopus 로고
    • Can MS fully exploit the benefits of fast chromatography?
    • Hopfgartner, G. Can MS fully exploit the benefits of fast chromatography? Bioanalysis 2011, 3, 121-123 10.4155/bio.10.191
    • (2011) Bioanalysis , vol.3 , pp. 121-123
    • Hopfgartner, G.1


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