-
1
-
-
0043198426
-
Proteomic tools for quantitation by mass spectrometry
-
Lill, J. (2003) Proteomic tools for quantitation by mass spectrometry. Mass Spectrom Rev 22, 182–194.
-
(2003)
Mass Spectrom Rev
, vol.22
, pp. 182-194
-
-
Lill, J.1
-
2
-
-
0038401326
-
Stable isotopic labeling and mass spectrometry as a means to determine differences in protein expression
-
Goodlett, D. R. and Yi, E. C. (2003) Stable isotopic labeling and mass spectrometry as a means to determine differences in protein expression. TrAC Trends Anal Chem 22, 282–290.
-
(2003)
Trac Trends Anal Chem
, vol.22
, pp. 282-290
-
-
Goodlett, D.R.1
Yi, E.C.2
-
3
-
-
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., and Ahn, N. G. (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4, 1487–1502.
-
(2005)
Mol Cell Proteomics
, vol.4
, 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
-
4
-
-
0031172203
-
Enhancement of the effective resolution of mass spectra of high-mass biomole-cules by maximum entropy-based deconvolution to eliminate the isotopic natural abundance distribution
-
Zhongqi, Z., Shenheng, G., and Marshall, A. G. (1997) Enhancement of the effective resolution of mass spectra of high-mass biomole-cules by maximum entropy-based deconvolution to eliminate the isotopic natural abundance distribution. J Am Soc Mass Spectrom 8, 659–670.
-
(1997)
J am Soc Mass Spectrom
, vol.8
, pp. 659-670
-
-
Zhongqi, Z.1
Shenheng, G.2
Marshall, A.G.3
-
6
-
-
33846651082
-
Difference detection in LC-MS data for protein biomarker discovery
-
Listgarten, J., Neal, R. M., Roweis, S. T., Wong, P., and Emili, A. (2007) Difference detection in LC-MS data for protein biomarker discovery. Bioinformatics 23, e198–e204.
-
(2007)
Bioinformatics
, vol.23
, pp. e198-e204
-
-
Listgarten, J.1
Neal, R.M.2
Roweis, S.T.3
Wong, P.4
Emili, A.5
-
7
-
-
34147109800
-
A statistical method for chromatographic alignment of LC-MS data
-
Wang, P., Tang, H., Fitzgibbon, M. P., McIntosh, M., Coram, M., Zhang, H., Yi, E., and Aebersold, R. (2007) A statistical method for chromatographic alignment of LC-MS data. Biostatistics 8, 357–367.
-
(2007)
Biostatistics
, vol.8
, pp. 357-367
-
-
Wang, P.1
Tang, H.2
Fitzgibbon, M.P.3
McIntosh, M.4
Coram, M.5
Zhang, H.6
Yi, E.7
Aebersold, R.8
-
8
-
-
6044226889
-
Differential mass spectrometry: A label-free LC-MS method for finding significant differences in complex peptide and protein mixtures
-
Wiener, M. C., Sachs, J. R., Deyanova, E. G., and Yates, N. A. (2004) Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal Chem 76, 6085–6096.
-
(2004)
Anal Chem
, vol.76
, pp. 6085-6096
-
-
Wiener, M.C.1
Sachs, J.R.2
Deyanova, E.G.3
Yates, N.A.4
-
9
-
-
14344250874
-
Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry
-
Radulovic, D., Jelveh, S., Ryu, S., Hamilton, T. G., Foss, E., Mao, Y., and Emili, A. (2004) Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 3, 984–997.
-
(2004)
Mol Cell Proteomics
, vol.3
, pp. 984-997
-
-
Radulovic, D.1
Jelveh, S.2
Ryu, S.3
Hamilton, T.G.4
Foss, E.5
Mao, Y.6
Emili, A.7
-
10
-
-
33845527323
-
ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces
-
Sadygov, R. G., Maroto, F. M., and Huhmer, A. F. (2006) ChromAlign: a two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces. Anal Chem 78, 8207–8217.
-
(2006)
Anal Chem
, vol.78
, pp. 8207-8217
-
-
Sadygov, R.G.1
Maroto, F.M.2
Huhmer, A.F.3
-
11
-
-
33645468005
-
Signal maps for mass spectrometry-based comparative proteomics
-
Prakash, A., Mallick, P., Whiteaker, J., Zhang, H., Paulovich, A., Flory, M., Lee, H., Aebersold, R., and Schwikowski, B. (2006) Signal maps for mass spectrometry-based comparative proteomics. Mol Cell Proteomics 5, 423–432.
-
(2006)
Mol Cell Proteomics
, vol.5
, pp. 423-432
-
-
Prakash, A.1
Mallick, P.2
Whiteaker, J.3
Zhang, H.4
Paulovich, A.5
Flory, M.6
Lee, H.7
Aebersold, R.8
Schwikowski, B.9
-
12
-
-
33750743755
-
Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline
-
Jaitly, N., Monroe, M. E., Petyuk, V. A., Clauss, T. R., Adkins, J. N., and Smith, R. D. (2006) Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline. Anal Chem 78, 7397–7409.
-
(2006)
Anal Chem
, vol.78
, pp. 7397-7409
-
-
Jaitly, N.1
Monroe, M.E.2
Petyuk, V.A.3
Clauss, T.R.4
Adkins, J.N.5
Smith, R.D.6
-
13
-
-
32144446968
-
Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC-MS
-
America, A. H., Cordewener, J. H., van Geffen, M. H., Lommen, A., Vissers, J. P., Bino, R. J., and Hall, R. D. (2006) Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC-MS. Proteomics 6, 641–653.
-
(2006)
Proteomics
, vol.6
, pp. 641-653
-
-
America, A.H.1
Cordewener, J.H.2
van Geffen, M.H.3
Lommen, A.4
Vissers, J.P.5
Bino, R.J.6
Hall, R.D.7
-
14
-
-
28544448710
-
A comprehensive two-dimensional retention time alignment algorithm to enhance chemometric analysis of comprehensive two-dimensional separation data
-
Pierce, K. M., Wood, L. F., Wright, B. W., and Synovec, R. E. (2005) A comprehensive two-dimensional retention time alignment algorithm to enhance chemometric analysis of comprehensive two-dimensional separation data. Anal Chem 77, 7735–7743.
-
(2005)
Anal Chem
, vol.77
, pp. 7735-7743
-
-
Pierce, K.M.1
Wood, L.F.2
Wright, B.W.3
Synovec, R.E.4
-
15
-
-
37149014099
-
Chip-LC-MS for label-free profiling of human serum
-
Horvatovich, P., Govorukhina, N. I., Reijmers, T. H., van der Zee, A. G. J., Suits, F., and Bischoff, R. P. H. (2007) Chip-LC-MS for label-free profiling of human serum. Electrophoresis 28, 4493–4505.
-
(2007)
Electrophoresis
, vol.28
, pp. 4493-4505
-
-
Horvatovich, P.1
Govorukhina, N.I.2
Reijmers, T.H.3
van der Zee, A.G.J.4
Suits, F.5
Bischoff, R.P.H.6
-
16
-
-
35348965139
-
SuperHirn – a novel tool for high resolution LC-MS-based peptide/protein profiling
-
Mueller, L. N., Rinner, O., Schmidt, A., Letarte, S., Bodenmiller, B., Brusniak, M. Y., Vitek, O., Aebersold, R., and Muller, M. (2007) SuperHirn – a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 7, 3470–3480.
-
(2007)
Proteomics
, vol.7
, pp. 3470-3480
-
-
Mueller, L.N.1
Rinner, O.2
Schmidt, A.3
Letarte, S.4
Bodenmiller, B.5
Brusniak, M.Y.6
Vitek, O.7
Aebersold, R.8
Muller, M.9
-
17
-
-
84898983966
-
Multiple alignment of continuous time series
-
Listgarten, J., Neal, R. M., Roweis, S. T., and Emily, A. (2005) Multiple alignment of continuous time series. Neural Inf Process Syst 17, 817–824.
-
(2005)
Neural Inf Process Syst
, vol.17
, pp. 817-824
-
-
Listgarten, J.1
Neal, R.M.2
Roweis, S.T.3
Emily, A.4
-
18
-
-
61849127833
-
-
Vancouver, BC
-
Befekadu, G. K., Tadesse, M. G., Hathout, Y., and Ressom, H. W. (2008) Multiclass alignment of LC-MS data using probabilistic-based mixture regression models. Proceedings of the 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Vancouver, BC, 4094–4097.
-
(2008)
Multiclass Alignment of LC-MS Data Using Probabilistic-Based Mixture Regression Models. Proceedings of the 30Th Annual International Conference of the IEEE Engineering in Medicine and Biology Society
, pp. 4094-4097
-
-
Befekadu, G.K.1
Tadesse, M.G.2
Hathout, Y.3
Ressom, H.W.4
-
19
-
-
70350350388
-
Analysis of LC-MS data using probabilistic-based mixture regression models
-
Ressom, H. W., Befekadu, G. K., and Tadesse, M. G. (2009) Analysis of LC-MS data using probabilistic-based mixture regression models. at – Automatisierungstechnik 57, 453–465.
-
(2009)
At – Automatisierungstechnik
, vol.57
, pp. 453-465
-
-
Ressom, H.W.1
Befekadu, G.K.2
Tadesse, M.G.3
-
20
-
-
0002629270
-
Maximum likelihood from incomplete data via the EM algorithm
-
Dempster, A. P., Laird, N. M., and Rubin, D. B. (1977) Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc Series B (Methodol) 39, 1–38.
-
(1977)
J R Stat Soc Series B (Methodol)
, vol.39
, pp. 1-38
-
-
Dempster, A.P.1
Laird, N.M.2
Rubin, D.B.3
-
21
-
-
0000262562
-
Hierarchical mixtures of experts and the EM algorithm
-
Jordan, M. I. and Jacobs, R. A. (1994) Hierarchical mixtures of experts and the EM algorithm. Neural Comput 6, 181–214.
-
(1994)
Neural Comput
, vol.6
, pp. 181-214
-
-
Jordan, M.I.1
Jacobs, R.A.2
-
22
-
-
0021404166
-
Mixture densities, maximum likelihood and the EM algorithm
-
Redner, R. A. and Walker, H. F. (1984) Mixture densities, maximum likelihood and the EM algorithm. SIAM Rev 26, 195–239.
-
(1984)
SIAM Rev
, vol.26
, pp. 195-239
-
-
Redner, R.A.1
Walker, H.F.2
-
23
-
-
25444526868
-
Processing methods for differential analysis of LC/MS profile data
-
Katajamaa, M. and Oresic, M. (2005) Processing methods for differential analysis of LC/MS profile data. BMC Bioinformatics 6, 179.
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Katajamaa, M.1
Oresic, M.2
-
24
-
-
34347384910
-
Normalization method for metabolomics data using optimal selection of multiple internal standards
-
Sysi-Aho, M., Katajamaa, M., Yetukuri, L., and Oresic, M. (2007) Normalization method for metabolomics data using optimal selection of multiple internal standards. BMC Bioinformatics 8, 93.
-
(2007)
BMC Bioinformatics
, vol.8
-
-
Sysi-Aho, M.1
Katajamaa, M.2
Yetukuri, L.3
Oresic, M.4
-
25
-
-
70349885489
-
Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition
-
Karpievitch, Y. V., Taverner, T., Adkins, J. N., Callister, S. J., Anderson, G. A., Smith, R. D., and Dabney, A. R. (2009) Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition. Bioinformatics 25, 2573–2580.
-
(2009)
Bioinformatics
, vol.25
, pp. 2573-2580
-
-
Karpievitch, Y.V.1
Taverner, T.2
Adkins, J.N.3
Callister, S.J.4
Anderson, G.A.5
Smith, R.D.6
Dabney, A.R.7
-
26
-
-
1342294092
-
Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
-
Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30, e15.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. e15
-
-
Yang, Y.H.1
Dudoit, S.2
Luu, P.3
Lin, D.M.4
Peng, V.5
Ngai, J.6
Speed, T.P.7
-
27
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
Bolstad, B. M., Irizarry, R. A., Astrand, M., and Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185–193.
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
28
-
-
0034927555
-
Analysis of variance for gene expression microarray data
-
Kerr, M. K., Martin, M., and Churchill, G. A. (2000) Analysis of variance for gene expression microarray data. J Comput Biol 7, 819–837.
-
(2000)
J Comput Biol
, vol.7
, pp. 819-837
-
-
Kerr, M.K.1
Martin, M.2
Churchill, G.A.3
-
29
-
-
38649095350
-
A statistical model for iTRAQ data analysis
-
Hill, E. G., Schwacke, J. H., Comte-Walters, S., Slate, E. H., Oberg, A. L., Eckel-Passow, J. E., Therneau, T. M., and Schey, K. L. (2008) A statistical model for iTRAQ data analysis. J Proteome Res 7, 3091–3101.
-
(2008)
J Proteome Res
, vol.7
, pp. 3091-3101
-
-
Hill, E.G.1
Schwacke, J.H.2
Comte-Walters, S.3
Slate, E.H.4
Oberg, A.L.5
Eckel-Passow, J.E.6
Therneau, T.M.7
Schey, K.L.8
-
30
-
-
0141743615
-
Discriminant models for high-throughput proteomics mass spectrometer data
-
Purohit, P. V. and Rocke, D. M. (2003) Discriminant models for high-throughput proteomics mass spectrometer data. Proteomics 3, 1699–1703.
-
(2003)
Proteomics
, vol.3
, pp. 1699-1703
-
-
Purohit, P.V.1
Rocke, D.M.2
-
31
-
-
34548388291
-
LC-MS-based metabolomics in drug metabolism
-
Chen, C., Gonzalez, F. J., and Idle, J. R. (2007) LC-MS-based metabolomics in drug metabolism. Drug Metab Rev 39, 581–597.
-
(2007)
Drug Metab Rev
, vol.39
, pp. 581-597
-
-
Chen, C.1
Gonzalez, F.J.2
Idle, J.R.3
-
32
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B 57, 289–300.
-
(1995)
J R Stat Soc Series B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
33
-
-
85139032836
-
Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach. Stat Appl Genet Mol Biol 6
-
Opgen-Rhein, R. and Strimmer, K. (2007) Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach. Stat Appl Genet Mol Biol 6, Article9.
-
(2007)
Article9
-
-
Opgen-Rhein, R.1
Strimmer, K.2
-
34
-
-
85139011041
-
Classification of breast cancer versus normal samples from mass spectrometry profiles using linear discriminant analysis of important features selected by random forest. Stat Appl Genet Mol Biol 7
-
Datta, S. (2008) Classification of breast cancer versus normal samples from mass spectrometry profiles using linear discriminant analysis of important features selected by random forest. Stat Appl Genet Mol Biol 7, Article7.
-
(2008)
Article7
-
-
Datta, S.1
-
35
-
-
0141738784
-
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
-
Wu, B., Abbott, T., Fishman, D., McMurray, W., Mor, G., Stone, K., Ward, D., Williams, K., and Zhao, H. (2003) Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics 19, 1636–1643.
-
(2003)
Bioinformatics
, vol.19
, pp. 1636-1643
-
-
Wu, B.1
Abbott, T.2
Fishman, D.3
McMurray, W.4
Mor, G.5
Stone, K.6
Ward, D.7
Williams, K.8
Zhao, H.9
-
36
-
-
0036161259
-
Gene Selection for cancer classification using support vector machines
-
Guyon, I., Weston, J., Barnhill, S., and Vapnik, V. (2002) Gene Selection for cancer classification using support vector machines. Mach Learn 46, 389–422.
-
(2002)
Mach Learn
, vol.46
, pp. 389-422
-
-
Guyon, I.1
Weston, J.2
Barnhill, S.3
Vapnik, V.4
-
37
-
-
34047103028
-
Peak selection from MALDI-TOF mass spectra using ant colony optimization
-
Ressom, H. W., Varghese, R. S., Drake, S. K., Hortin, G. L., Abdel-Hamid, M., Loffredo, C. A., and Goldman, R. (2007) Peak selection from MALDI-TOF mass spectra using ant colony optimization. Bioinformatics 23, 619–626.
-
(2007)
Bioinformatics
, vol.23
, pp. 619-626
-
-
Ressom, H.W.1
Varghese, R.S.2
Drake, S.K.3
Hortin, G.L.4
Abdel-Hamid, M.5
Loffredo, C.A.6
Goldman, R.7
-
38
-
-
33645097857
-
Optimized multilayer percep-trons for molecular classification and diagnosis using genomic data
-
Wang, Z., Wang, Y., Xuan, J., Dong, Y., Bakay, M., Feng, Y., Clarke, R., and Hoffman, E. P. (2006) Optimized multilayer percep-trons for molecular classification and diagnosis using genomic data. Bioinformatics 22, 755–761.
-
(2006)
Bioinformatics
, vol.22
, pp. 755-761
-
-
Wang, Z.1
Wang, Y.2
Xuan, J.3
Dong, Y.4
Bakay, M.5
Feng, Y.6
Clarke, R.7
Hoffman, E.P.8
-
39
-
-
26444560679
-
Cancer proteomics: In pursuit of “true” biomarker discovery
-
Zhang, Z. and Chan, D. W. (2005) Cancer proteomics: in pursuit of “true” biomarker discovery. Cancer Epidemiol Biomarkers Prev 14, 2283–2286.
-
(2005)
Cancer Epidemiol Biomarkers Prev
, vol.14
, pp. 2283-2286
-
-
Zhang, Z.1
Chan, D.W.2
|