-
1
-
-
0035106351
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
8
-
-
57049106891
-
An Integrated, Directed Mass Spectrometric Approach for In-depth Characterization of Complex Peptide Mixtures
-
Schmidt, A.; Gehlenborg, N.; Bodenmiller, B.; Mueller, L. N.; Campbell, D.; Mueller, M.; Aebersold, R.; Domon, B. An Integrated, Directed Mass Spectrometric Approach for In-depth Characterization of Complex Peptide Mixtures Mol. Cell. Proteomics 2008, 7, 2138-2150 10.1074/mcp.M700498-MCP200
-
(2008)
Mol. Cell. Proteomics
, vol.7
, pp. 2138-2150
-
-
Schmidt, A.1
Gehlenborg, N.2
Bodenmiller, B.3
Mueller, L.N.4
Campbell, D.5
Mueller, M.6
Aebersold, R.7
Domon, B.8
-
9
-
-
3242731195
-
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
-
10
-
-
76149142168
-
Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry
-
Tabb, D. L.; Vega-Montoto, L.; Rudnick, P. A.; Variyath, A. M.; Ham, A. J.; Bunk, D. M.; Kilpatrick, L. E.; Billheimer, D. D.; Blackman, R. K.; Cardasis, H. L.; Carr, S. A.; Clauser, K. R.; Jaffe, J. D.; Kowalski, K. A.; Neubert, T. A.; Regnier, F. E.; Schilling, B.; Tegeler, T. J.; Wang, M.; Wang, P.; Whiteaker, J. R.; Zimmerman, L. J.; Fisher, S. J.; Gibson, B. W.; Kinsinger, C. R.; Mesri, M.; Rodriguez, H.; Stein, S. E.; Tempst, P.; Paulovich, A. G.; Liebler, D. C.; Spiegelman, C. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry J. Proteome Res. 2010, 9, 761-776 10.1021/pr9006365
-
(2010)
J. Proteome Res.
, vol.9
, pp. 761-776
-
-
Tabb, D.L.1
Vega-Montoto, L.2
Rudnick, P.A.3
Variyath, A.M.4
Ham, A.J.5
Bunk, D.M.6
Kilpatrick, L.E.7
Billheimer, D.D.8
Blackman, R.K.9
Cardasis, H.L.10
Carr, S.A.11
Clauser, K.R.12
Jaffe, J.D.13
Kowalski, K.A.14
Neubert, T.A.15
Regnier, F.E.16
Schilling, B.17
Tegeler, T.J.18
Wang, M.19
Wang, P.20
Whiteaker, J.R.21
Zimmerman, L.J.22
Fisher, S.J.23
Gibson, B.W.24
Kinsinger, C.R.25
Mesri, M.26
Rodriguez, H.27
Stein, S.E.28
Tempst, P.29
Paulovich, A.G.30
Liebler, D.C.31
Spiegelman, C.32
more..
-
11
-
-
84924712451
-
Processing strategies and software solutions for data-independent acquisition in mass spectrometry
-
Bilbao, A.; Varesio, E.; Luban, J.; Strambio-De-Castillia, C.; Hopfgartner, G.; Muller, M.; Lisacek, F. Processing strategies and software solutions for data-independent acquisition in mass spectrometry Proteomics 2015, 15, 964-980 10.1002/pmic.201400323
-
(2015)
Proteomics
, vol.15
, pp. 964-980
-
-
Bilbao, A.1
Varesio, E.2
Luban, J.3
Strambio-De-Castillia, C.4
Hopfgartner, G.5
Muller, M.6
Lisacek, F.7
-
12
-
-
14744293536
-
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
-
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
-
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
-
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
-
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
-
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
-
18
-
-
84876337044
-
Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS
-
Liu, Y.; Huttenhain, R.; Surinova, S.; Gillet, L. C.; Mouritsen, J.; Brunner, R.; Navarro, P.; Aebersold, R. Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS Proteomics 2013, 13, 1247-1256 10.1002/pmic.201200417
-
(2013)
Proteomics
, vol.13
, pp. 1247-1256
-
-
Liu, Y.1
Huttenhain, R.2
Surinova, S.3
Gillet, L.C.4
Mouritsen, J.5
Brunner, R.6
Navarro, P.7
Aebersold, R.8
-
19
-
-
84888858053
-
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
-
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
-
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
-
22
-
-
77951965920
-
Skyline: An open source document editor for creating and analyzing targeted proteomics experiments
-
MacLean, B.; Tomazela, D. M.; Shulman, N.; Chambers, M.; Finney, G. L.; Frewen, B.; Kern, R.; Tabb, D. L.; Liebler, D. C.; MacCoss, M. J. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments Bioinformatics 2010, 26, 966-968 10.1093/bioinformatics/btq054
-
(2010)
Bioinformatics
, vol.26
, pp. 966-968
-
-
MacLean, B.1
Tomazela, D.M.2
Shulman, N.3
Chambers, M.4
Finney, G.L.5
Frewen, B.6
Kern, R.7
Tabb, D.L.8
Liebler, D.C.9
MacCoss, M.J.10
-
23
-
-
55249121202
-
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
-
24
-
-
84860869167
-
Using iRT, a normalized retention time for more targeted measurement of peptides
-
Escher, C.; Reiter, L.; MacLean, B.; Ossola, R.; Herzog, F.; Chilton, J.; MacCoss, M. J.; Rinner, O. Using iRT, a normalized retention time for more targeted measurement of peptides Proteomics 2012, 12, 1111-1121 10.1002/pmic.201100463
-
(2012)
Proteomics
, vol.12
, pp. 1111-1121
-
-
Escher, C.1
Reiter, L.2
MacLean, B.3
Ossola, R.4
Herzog, F.5
Chilton, J.6
MacCoss, M.J.7
Rinner, O.8
-
25
-
-
79955595074
-
MProphet: Automated data processing and statistical validation for large-scale SRM experiments
-
Reiter, L.; Rinner, O.; Picotti, P.; Huttenhain, R.; Beck, M.; Brusniak, M.-Y.; Hengartner, M. O.; Aebersold, R. mProphet: automated data processing and statistical validation for large-scale SRM experiments Nat. Methods 2011, 8, 430-435 10.1038/nmeth.1584
-
(2011)
Nat. Methods
, vol.8
, pp. 430-435
-
-
Reiter, L.1
Rinner, O.2
Picotti, P.3
Huttenhain, R.4
Beck, M.5
Brusniak, M.-Y.6
Hengartner, M.O.7
Aebersold, R.8
-
26
-
-
84904094826
-
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
-
27
-
-
84942919548
-
SWATH libraries and common fragment libraries for metabolites identification in urine
-
In; Baltimore, USA.
-
Hopfgartner, G.; Varesio, E.; Burton, L.; Duchoslav, E.; Bonner, R. SWATH libraries and common fragment libraries for metabolites identification in urine. In 62nd ASMS Conference on Mass Spectrometry and Allied Topics; Baltimore, USA, 2014.
-
(2014)
62nd ASMS Conference on Mass Spectrometry and Allied Topics
-
-
Hopfgartner, G.1
Varesio, E.2
Burton, L.3
Duchoslav, E.4
Bonner, R.5
-
28
-
-
79951901773
-
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
-
29
-
-
77952205557
-
Global metabolic profiling procedures for urine using UPLC-MS
-
Want, E. J.; Wilson, I. D.; Gika, H.; Theodoridis, G.; Plumb, R. S.; Shockcor, J.; Holmes, E.; Nicholson, J. K. Global metabolic profiling procedures for urine using UPLC-MS Nat. Protoc. 2010, 5, 1005-1018 10.1038/nprot.2010.50
-
(2010)
Nat. Protoc.
, vol.5
, pp. 1005-1018
-
-
Want, E.J.1
Wilson, I.D.2
Gika, H.3
Theodoridis, G.4
Plumb, R.S.5
Shockcor, J.6
Holmes, E.7
Nicholson, J.K.8
|