-
1
-
-
77149162668
-
Peptide and protein quantification: A map of the minefield
-
Vaudel, M.; Sickmann, A.; Martens, L. Peptide and protein quantification: A map of the minefield Proteomics 2010, 10 (4) 650-670
-
(2010)
Proteomics
, vol.10
, Issue.4
, pp. 650-670
-
-
Vaudel, M.1
Sickmann, A.2
Martens, L.3
-
2
-
-
79958134282
-
Monitoring protein expression in whole-cell extracts by targeted label- and standard-free LC-MS/MS
-
Bluemlein, K.; Ralser, M. Monitoring protein expression in whole-cell extracts by targeted label- and standard-free LC-MS/MS Nat. Protoc. 2011, 6 (6) 859-869
-
(2011)
Nat. Protoc.
, vol.6
, Issue.6
, pp. 859-869
-
-
Bluemlein, K.1
Ralser, M.2
-
3
-
-
84907197082
-
Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ
-
Cox, J.; Hein, M. Y.; Luber, C. A.; Paron, I.; Nagaraj, N.; Mann, M. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ Mol. Cell. Proteomics 2014, 13 (9) 2513-2526
-
(2014)
Mol. Cell. Proteomics
, vol.13
, Issue.9
, pp. 2513-2526
-
-
Cox, J.1
Hein, M.Y.2
Luber, C.A.3
Paron, I.4
Nagaraj, N.5
Mann, M.6
-
4
-
-
84885234215
-
Quantitative Proteomic Analysis of Microdissected Breast Cancer Tissues: Comparison of Label-Free and SILAC-based Quantification with Shotgun, Directed, and Targeted MS Approaches
-
Liu, N. Q.; Dekker, L. J. M.; Stingl, C.; Güzel, C.; De Marchi, T.; Martens, J. W. M.; Foekens, J. A.; Luider, T. M.; Umar, A. Quantitative Proteomic Analysis of Microdissected Breast Cancer Tissues: Comparison of Label-Free and SILAC-based Quantification with Shotgun, Directed, and Targeted MS Approaches J. Proteome Res. 2013, 12 (10) 4627-4641
-
(2013)
J. Proteome Res.
, vol.12
, Issue.10
, pp. 4627-4641
-
-
Liu, N.Q.1
Dekker, L.J.M.2
Stingl, C.3
Güzel, C.4
De Marchi, T.5
Martens, J.W.M.6
Foekens, J.A.7
Luider, T.M.8
Umar, A.9
-
5
-
-
79953184318
-
Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes
-
Mosley, A. L.; Sardiu, M. E.; Pattenden, S. G.; Workman, J. L.; Florens, L.; Washburn, M. P. Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes Mol. Cell. Proteomics 2011, 10.1074/mcp.M110.000687
-
(2011)
Mol. Cell. Proteomics
-
-
Mosley, A.L.1
Sardiu, M.E.2
Pattenden, S.G.3
Workman, J.L.4
Florens, L.5
Washburn, M.P.6
-
6
-
-
33646564676
-
Label-Free Protein Quantification Using LC-Coupled Ion Trap or FT Mass Spectrometry: Reproducibility, Linearity, and Application with Complex Proteomes
-
Wang, G.; Wu, W. W.; Zeng, W.; Chou, C.-L.; Shen, R.-F. Label-Free Protein Quantification Using LC-Coupled Ion Trap or FT Mass Spectrometry: Reproducibility, Linearity, and Application with Complex Proteomes J. Proteome Res. 2006, 5 (5) 1214-1223
-
(2006)
J. Proteome Res.
, vol.5
, Issue.5
, pp. 1214-1223
-
-
Wang, G.1
Wu, W.W.2
Zeng, W.3
Chou, C.-L.4
Shen, R.-F.5
-
7
-
-
31644446949
-
Absolute Quantification of Proteins by LCMSE: A Virtue of Parallel ms Acquisition
-
Silva, J. C.; Gorenstein, M. V.; Li, G.-Z.; Vissers, J. P. C.; Geromanos, S. J. Absolute Quantification of Proteins by LCMSE: A Virtue of Parallel ms Acquisition Mol. Cell. Proteomics 2006, 5 (1) 144-156
-
(2006)
Mol. Cell. Proteomics
, vol.5
, Issue.1
, pp. 144-156
-
-
Silva, J.C.1
Gorenstein, M.V.2
Li, G.-Z.3
Vissers, J.P.C.4
Geromanos, S.J.5
-
8
-
-
84870596405
-
Current methods for global proteome identification
-
Vaudel, M.; Sickmann, A.; Martens, L. Current methods for global proteome identification Expert Rev. Proteomics 2012, 9 (5) 519-532
-
(2012)
Expert Rev. Proteomics
, vol.9
, Issue.5
, pp. 519-532
-
-
Vaudel, M.1
Sickmann, A.2
Martens, L.3
-
9
-
-
84861990031
-
Protease bias in absolute protein quantitation
-
Peng, M.; Taouatas, N.; Cappadona, S.; van Breukelen, B.; Mohammed, S.; Scholten, A.; Heck, A. J. R. Protease bias in absolute protein quantitation Nat. Methods 2012, 9 (6) 524-525
-
(2012)
Nat. Methods
, vol.9
, Issue.6
, pp. 524-525
-
-
Peng, M.1
Taouatas, N.2
Cappadona, S.3
Van Breukelen, B.4
Mohammed, S.5
Scholten, A.6
Heck, A.J.R.7
-
10
-
-
84893847165
-
Quantifying the Effect of Competition for Detection between Coeluting Peptides on Detection Probabilities in Mass-Spectrometry-Based Proteomics
-
Schliekelman, P.; Liu, S. Quantifying the Effect of Competition for Detection between Coeluting Peptides on Detection Probabilities in Mass-Spectrometry-Based Proteomics J. Proteome Res. 2013, 13 (2) 348-361
-
(2013)
J. Proteome Res.
, vol.13
, Issue.2
, pp. 348-361
-
-
Schliekelman, P.1
Liu, S.2
-
11
-
-
67349208911
-
Bioinformatics analysis of mass spectrometry-based proteomics data sets
-
Kumar, C.; Mann, M. Bioinformatics analysis of mass spectrometry-based proteomics data sets FEBS Lett. 2009, 583 (11) 1703-1712
-
(2009)
FEBS Lett.
, vol.583
, Issue.11
, pp. 1703-1712
-
-
Kumar, C.1
Mann, M.2
-
12
-
-
3242731195
-
A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics
-
Liu, H.; Sadygov, R. G.; Yates, J. R. A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics Anal. Chem. 2004, 76 (14) 4193-4201
-
(2004)
Anal. Chem.
, vol.76
, Issue.14
, pp. 4193-4201
-
-
Liu, H.1
Sadygov, R.G.2
Yates, J.R.3
-
13
-
-
34748916981
-
Quantitative mass spectrometry in proteomics: A critical review
-
Bantscheff, M.; Schirle, M.; Sweetman, G.; Rick, J.; Kuster, B. Quantitative mass spectrometry in proteomics: a critical review Anal. Bioanal. Chem. 2007, 389 (4) 1017-31
-
(2007)
Anal. Bioanal. Chem.
, vol.389
, Issue.4
, pp. 1017-1031
-
-
Bantscheff, M.1
Schirle, M.2
Sweetman, G.3
Rick, J.4
Kuster, B.5
-
14
-
-
38649095599
-
An Assessment of Software Solutions for the Analysis of Mass Spectrometry Based Quantitative Proteomics Data
-
Mueller, L. N.; Brusniak, M.-Y.; Mani, D. R.; Aebersold, R. An Assessment of Software Solutions for the Analysis of Mass Spectrometry Based Quantitative Proteomics Data J. Proteome Res. 2008, 7 (1) 51-61
-
(2008)
J. Proteome Res.
, vol.7
, Issue.1
, pp. 51-61
-
-
Mueller, L.N.1
Brusniak, M.-Y.2
Mani, D.R.3
Aebersold, R.4
-
15
-
-
27644543078
-
Comparison of Label-free Methods for Quantifying Human Proteins by Shotgun Proteomics
-
Old, W. M.; Meyer-Arendt, K.; Aveline-Wolf, L.; Pierce, K. G.; Mendoza, A.; Sevinsky, J. R.; Resing, K. A.; Ahn, N. G. Comparison of Label-free Methods for Quantifying Human Proteins by Shotgun Proteomics Mol. Cell. Proteomics 2005, 4 (10) 1487-1502
-
(2005)
Mol. Cell. Proteomics
, vol.4
, Issue.10
, pp. 1487-1502
-
-
Old, W.M.1
Meyer-Arendt, K.2
Aveline-Wolf, L.3
Pierce, K.G.4
Mendoza, A.5
Sevinsky, J.R.6
Resing, K.A.7
Ahn, N.G.8
-
16
-
-
84891759563
-
Label-free Quantitative Protein Profiling of vastus lateralis Muscle during Human Aging
-
Théron, L.; Gueugneau, M.; Coudy, C.; Viala, D.; Bijlsma, A.; Butler-Browne, G.; Maier, A.; Béchet, D.; Chambon, C. Label-free Quantitative Protein Profiling of vastus lateralis Muscle During Human Aging Mol. Cell. Proteomics 2014, 13 (1) 283-294
-
(2014)
Mol. Cell. Proteomics
, vol.13
, Issue.1
, pp. 283-294
-
-
Théron, L.1
Gueugneau, M.2
Coudy, C.3
Viala, D.4
Bijlsma, A.5
Butler-Browne, G.6
Maier, A.7
Béchet, D.8
Chambon, C.9
-
17
-
-
77952344256
-
Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions
-
Hubner, N. C.; Bird, A. W.; Cox, J.; Splettstoesser, B.; Bandilla, P.; Poser, I.; Hyman, A.; Mann, M. Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions J. Cell Biol. 2010, 189 (4) 739-754
-
(2010)
J. Cell Biol.
, vol.189
, Issue.4
, pp. 739-754
-
-
Hubner, N.C.1
Bird, A.W.2
Cox, J.3
Splettstoesser, B.4
Bandilla, P.5
Poser, I.6
Hyman, A.7
Mann, M.8
-
18
-
-
70449433751
-
Protein Quantification in Label-Free LC-MS Experiments
-
Clough, T.; Key, M.; Ott, I.; Ragg, S.; Schadow, G.; Vitek, O. Protein Quantification in Label-Free LC-MS Experiments J. Proteome Res. 2009, 8 (11) 5275-5284
-
(2009)
J. Proteome Res.
, vol.8
, Issue.11
, pp. 5275-5284
-
-
Clough, T.1
Key, M.2
Ott, I.3
Ragg, S.4
Schadow, G.5
Vitek, O.6
-
19
-
-
68549137863
-
A statistical framework for protein quantitation in bottom-up MS-based proteomics
-
Karpievitch, Y.; Stanley, J.; Taverner, T.; Huang, J.; Adkins, J. N.; Ansong, C.; Heffron, F.; Metz, T. O.; Qian, W.-J.; Yoon, H.; Smith, R. D.; Dabney, A. R. A statistical framework for protein quantitation in bottom-up MS-based proteomics Bioinformatics 2009, 25 (16) 2028-2034
-
(2009)
Bioinformatics
, vol.25
, Issue.16
, pp. 2028-2034
-
-
Karpievitch, Y.1
Stanley, J.2
Taverner, T.3
Huang, J.4
Adkins, J.N.5
Ansong, C.6
Heffron, F.7
Metz, T.O.8
Qian, W.-J.9
Yoon, H.10
Smith, R.D.11
Dabney, A.R.12
-
20
-
-
76649122499
-
Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance
-
Paulovich, A. G.; Billheimer, D.; Ham, A.-J. L.; Vega-Montoto, L.; Rudnick, P. A.; Tabb, D. L.; Wang, P.; Blackman, R. K.; Bunk, D. M.; Cardasis, H. L.; Clauser, K. R.; Kinsinger, C. R.; Schilling, B.; Tegeler, T. J.; Variyath, A. M.; Wang, M.; Whiteaker, J. R.; Zimmerman, L. J.; Fenyo, D.; Carr, S. A.; Fisher, S. J.; Gibson, B. W.; Mesri, M.; Neubert, T. A.; Regnier, F. E.; Rodriguez, H.; Spiegelman, C.; Stein, S. E.; Tempst, P.; Liebler, D. C. Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance Mol. Cell. Proteomics 2010, 9 (2) 242-254
-
(2010)
Mol. Cell. Proteomics
, vol.9
, Issue.2
, pp. 242-254
-
-
Paulovich, A.G.1
Billheimer, D.2
Ham, A.-J.L.3
Vega-Montoto, L.4
Rudnick, P.A.5
Tabb, D.L.6
Wang, P.7
Blackman, R.K.8
Bunk, D.M.9
Cardasis, H.L.10
Clauser, K.R.11
Kinsinger, C.R.12
Schilling, B.13
Tegeler, T.J.14
Variyath, A.M.15
Wang, M.16
Whiteaker, J.R.17
Zimmerman, L.J.18
Fenyo, D.19
Carr, S.A.20
Fisher, S.J.21
Gibson, B.W.22
Mesri, M.23
Neubert, T.A.24
Regnier, F.E.25
Rodriguez, H.26
Spiegelman, C.27
Stein, S.E.28
Tempst, P.29
Liebler, D.C.30
more..
-
21
-
-
84907197082
-
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ
-
Cox, J.; Hein, M. Y.; Luber, C. A.; Paron, I.; Nagaraj, N.; Mann, M. Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ Mol. Cell. Proteomics 2014, 13 (9) 2513-2526
-
(2014)
Mol. Cell. Proteomics
, vol.13
, Issue.9
, pp. 2513-2526
-
-
Cox, J.1
Hein, M.Y.2
Luber, C.A.3
Paron, I.4
Nagaraj, N.5
Mann, M.6
-
22
-
-
57449099865
-
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 (12) 1367-1372
-
(2008)
Nat. Biotechnol.
, vol.26
, Issue.12
, pp. 1367-1372
-
-
Cox, J.1
Mann, M.2
-
23
-
-
0001677717
-
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
-
Benjamini, Y.; Hochberg, Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing J. R. Stat. Soc.: Series B 1995, 57 (1) 289-300
-
(1995)
J. R. Stat. Soc.: Series B
, vol.57
, Issue.1
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
24
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments.
-
Article 3
-
Smyth, G. K., Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl. Genet. Mol. Biol. 2004, 3, Article 3.
-
(2004)
Stat Appl. Genet. Mol. Biol.
, vol.3
-
-
Smyth, G.K.1
-
25
-
-
84872636119
-
An approximate distribution of estimates of variance components
-
Satterthwaite, F. E. An approximate distribution of estimates of variance components Biometrics 1946, 2 (6) 110-4
-
(1946)
Biometrics
, vol.2
, Issue.6
, pp. 110-114
-
-
Satterthwaite, F.E.1
-
26
-
-
38649098134
-
Does Trypsin Cut before Proline?
-
Rodriguez, J.; Gupta, N.; Smith, R. D.; Pevzner, P. A. Does Trypsin Cut Before Proline? J. Proteome Res. 2008, 7 (1) 300-305
-
(2008)
J. Proteome Res.
, vol.7
, Issue.1
, pp. 300-305
-
-
Rodriguez, J.1
Gupta, N.2
Smith, R.D.3
Pevzner, P.A.4
-
27
-
-
81555215473
-
Peptide polarity and the position of arginine as sources of selectivity during positive electrospray ionisation mass spectrometry
-
Abaye, D. A.; Pullen, F. S.; Nielsen, B. V. Peptide polarity and the position of arginine as sources of selectivity during positive electrospray ionisation mass spectrometry Rapid Commun. Mass Spectrom. 2011, 25 (23) 3597-3608
-
(2011)
Rapid Commun. Mass Spectrom.
, vol.25
, Issue.23
, pp. 3597-3608
-
-
Abaye, D.A.1
Pullen, F.S.2
Nielsen, B.V.3
|