-
1
-
-
5744223586
-
An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: Its application to protein peptide mapping by off-line HPLC-MALDI MS
-
Krokhin, O. V.; Craig, R.; Spicer, V.; Ens, W.; Standing, K. G.; Beavis, R. C.; Wilkins, J. A. An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: its application to protein peptide mapping by off-line HPLC-MALDI MS Mol. Cell. Proteomics 2004, 3, 908-919
-
(2004)
Mol. Cell. Proteomics
, vol.3
, pp. 908-919
-
-
Krokhin, O.V.1
Craig, R.2
Spicer, V.3
Ens, W.4
Standing, K.G.5
Beavis, R.C.6
Wilkins, J.A.7
-
2
-
-
33751208935
-
Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: Application to 300- and 100-A pore size C18 sorbents
-
Krokhin, O. V. Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: application to 300- and 100-A pore size C18 sorbents Anal. Chem. 2006, 78, 7785-7795
-
(2006)
Anal. Chem.
, vol.78
, pp. 7785-7795
-
-
Krokhin, O.V.1
-
3
-
-
33746448330
-
Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information
-
Petritis, K.; Kangas, L. J.; Yan, B.; Monroe, M. E.; Strittmatter, E. F.; Qian, W.-J.; Adkins, J. N.; Moore, R. J.; Xu, Y.; Lipton, M. S.; Camp, D. G.; Smith, R. D. Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information Anal. Chem. 2006, 78, 5026-5039
-
(2006)
Anal. Chem.
, vol.78
, pp. 5026-5039
-
-
Petritis, K.1
Kangas, L.J.2
Yan, B.3
Monroe, M.E.4
Strittmatter, E.F.5
Qian, W.-J.6
Adkins, J.N.7
Moore, R.J.8
Xu, Y.9
Lipton, M.S.10
Camp, D.G.11
Smith, R.D.12
-
4
-
-
4444350538
-
Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry
-
Strittmatter, E. F.; Kangas, L. J.; Petritis, K.; Mottaz, H. M.; Anderson, G. A.; Shen, Y.; Jacobs, J. M.; Camp, D. G.; Smith, R. D. Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry J. Proteome Res. 2004, 3, 760-769
-
(2004)
J. Proteome Res.
, vol.3
, pp. 760-769
-
-
Strittmatter, E.F.1
Kangas, L.J.2
Petritis, K.3
Mottaz, H.M.4
Anderson, G.A.5
Shen, Y.6
Jacobs, J.M.7
Camp, D.G.8
Smith, R.D.9
-
5
-
-
0037112383
-
Prediction of chromatographic retention and protein identification in liquid chromatography/mass spectrometry
-
Palmblad, M.; Ramstrom, M.; Markides, K.; Hakansson, P.; Bergquist, J. Prediction of chromatographic retention and protein identification in liquid chromatography/mass spectrometry Anal. Chem. 2002, 74, 5826-5830
-
(2002)
Anal. Chem.
, vol.74
, pp. 5826-5830
-
-
Palmblad, M.1
Ramstrom, M.2
Markides, K.3
Hakansson, P.4
Bergquist, J.5
-
6
-
-
34548041670
-
Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions
-
DOI 10.1021/ac070262k
-
Klammer, A. A.; Yi, X.; MacCoss, M. J.; Noble, W. S. Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions Anal. Chem. 2007, 79, 6111-6118 (Pubitemid 47282320)
-
(2007)
Analytical Chemistry
, vol.79
, Issue.16
, pp. 6111-6118
-
-
Klammer, A.A.1
Yi, X.2
MacCoss, M.J.3
Noble, W.S.4
-
7
-
-
68549125514
-
Improving Peptide Identification in Proteome Analysis by a Two-Dimensional Retention Time Filtering Approach
-
Pfeifer, N.; Leinenbach, A.; Huber, C.; Kohlbacher, O. Improving Peptide Identification in Proteome Analysis by a Two-Dimensional Retention Time Filtering Approach J. Proteome Res. 2009, 8, 4109-4115
-
(2009)
J. Proteome Res.
, vol.8
, pp. 4109-4115
-
-
Pfeifer, N.1
Leinenbach, A.2
Huber, C.3
Kohlbacher, O.4
-
8
-
-
0018990802
-
Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition
-
Meek, J. L. Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition Proc. Natl. Acad. Sci. U.S.A. 1980, 77, 1632-1636
-
(1980)
Proc. Natl. Acad. Sci. U.S.A.
, vol.77
, pp. 1632-1636
-
-
Meek, J.L.1
-
9
-
-
39849105680
-
Statistical learning of peptide retention behavior in chromatographic separations: A new kernel-based approach for computational proteomics
-
Pfeifer, N.; Leinenbach, A.; Huber, C.; Kohlbacher, O. Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics BMC Bioinf. 2007, 8, 468
-
(2007)
BMC Bioinf.
, vol.8
, pp. 468
-
-
Pfeifer, N.1
Leinenbach, A.2
Huber, C.3
Kohlbacher, O.4
-
10
-
-
0031888036
-
A. High throughput protein characterization by automated reverse-phase chromatography/electrospray tandem mass spectrometry
-
Ducret, A.; Van Oostveen, I.; Eng, J. K.; Yates, J. R., III; Aebersold, R. A. High throughput protein characterization by automated reverse-phase chromatography/electrospray tandem mass spectrometry Protein Sci. 1998, 7, 706-719
-
(1998)
Protein Sci.
, vol.7
, pp. 706-719
-
-
Ducret, A.1
Van Oostveen, I.2
Eng, J.K.3
Yates Iii, J.R.4
Aebersold, R.5
-
11
-
-
6344221680
-
Implications of new proteomics strategies for biology and medicine
-
Domon, B.; Broder, S. Implications of new proteomics strategies for biology and medicine J. Proteome Res. 2004, 3, 253-260
-
(2004)
J. Proteome Res.
, vol.3
, pp. 253-260
-
-
Domon, B.1
Broder, S.2
-
12
-
-
68949206409
-
Applying mass spectrometry-based proteomics to genetics, genomics and network biology
-
Gstaiger, M.; Aebersold, R. Applying mass spectrometry-based proteomics to genetics, genomics and network biology Nat. Rev. Genet. 2009, 10, 617-627
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 617-627
-
-
Gstaiger, M.1
Aebersold, R.2
-
13
-
-
67650564834
-
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma
-
Addona, T. A. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma Nat. Biotechnol. 2009, 27, 633-641
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 633-641
-
-
Addona, T.A.1
-
14
-
-
68749094119
-
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics
-
Picotti, P.; Bodenmiller, B.; Mueller, L.; Domon, B.; Aebersold, R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics Cell 2009, 138, 795-806
-
(2009)
Cell
, vol.138
, pp. 795-806
-
-
Picotti, P.1
Bodenmiller, B.2
Mueller, L.3
Domon, B.4
Aebersold, R.5
-
15
-
-
33645813378
-
Mass spectrometry and protein analysis
-
Domon, B.; Aebersold, R. Mass spectrometry and protein analysis Science 2006, 312, 212
-
(2006)
Science
, vol.312
, pp. 212
-
-
Domon, B.1
Aebersold, R.2
-
16
-
-
65449129054
-
Current affairs in quantitative targeted proteomics: Multiple reaction monitoring-mass spectrometry
-
Yocum, A. K.; Chinnaiyan, A. M. Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry Briefings Funct. Genomics Proteomics 2009, 8, 145-157
-
(2009)
Briefings Funct. Genomics Proteomics
, vol.8
, pp. 145-157
-
-
Yocum, A.K.1
Chinnaiyan, A.M.2
-
17
-
-
67049132416
-
Expediting the development of targeted SRM assays: Using data from shotgun proteomics to automate method development
-
Prakash, A.; Tomazela, D.; Frewen, B.; MacLean, B.; Merrihew, G.; Peterman, S.; MacCoss, M. Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development J. Proteome Res 2009, 8, 2733-2739
-
(2009)
J. Proteome Res
, vol.8
, pp. 2733-2739
-
-
Prakash, A.1
Tomazela, D.2
Frewen, B.3
MacLean, B.4
Merrihew, G.5
Peterman, S.6
MacCoss, M.7
-
18
-
-
77951965920
-
Skyline: An open source document editor for creating and analyzing targeted proteomics experiments
-
MacLean, B.; Tomazela, D.; Shulman, N.; Chambers, M.; Finney, G.; Frewen, B.; Kern, R.; Tabb, D.; Liebler, D.; MacCoss, M. Skyline: An open source document editor for creating and analyzing targeted proteomics experiments Bioinformatics 2010, 26, 966-968
-
(2010)
Bioinformatics
, vol.26
, pp. 966-968
-
-
MacLean, B.1
Tomazela, D.2
Shulman, N.3
Chambers, M.4
Finney, G.5
Frewen, B.6
Kern, R.7
Tabb, D.8
Liebler, D.9
MacCoss, M.10
-
19
-
-
0000857494
-
And others An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng, J.; McCormack, A.; Yates, J.; Eng, J. K.; McCormack, A. L.; Yates, J. R. and others An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database J. Am. Soc. Mass Spectrom. 1994, 5, 976-989
-
(1994)
J. Am. Soc. Mass Spectrom.
, vol.5
, pp. 976-989
-
-
Eng, J.1
McCormack, A.2
Yates, J.3
Eng, J.K.4
McCormack, A.L.5
Yates, J.R.6
-
20
-
-
76149132007
-
Comparison of database search strategies for high precursor mass accuracy MS/MS data
-
Hsieh, E.; Hoopmann, M.; MacLean, B.; MacCoss, M. Comparison of database search strategies for high precursor mass accuracy MS/MS data J. Proteome Res 2010, 9, 1138-1143
-
(2010)
J. Proteome Res
, vol.9
, pp. 1138-1143
-
-
Hsieh, E.1
Hoopmann, M.2
MacLean, B.3
MacCoss, M.4
-
21
-
-
35748972060
-
Semi-supervised learning for peptide identification from shotgun proteomics datasets
-
Käll, L.; Canterbury, J. D.; Weston, J.; Noble, W. S.; MacCoss, M. J. Semi-supervised learning for peptide identification from shotgun proteomics datasets Nat. Methods 2007, 4, 923-925
-
(2007)
Nat. Methods
, vol.4
, pp. 923-925
-
-
Käll, L.1
Canterbury, J.D.2
Weston, J.3
Noble, W.S.4
MacCoss, M.J.5
-
22
-
-
49549099563
-
Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry
-
Käll, L.; Storey, J.; Noble, W. Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry Bioinformatics 2008, 24, i42
-
(2008)
Bioinformatics
, vol.24
, pp. 42
-
-
Käll, L.1
Storey, J.2
Noble, W.3
-
23
-
-
0020427613
-
The isolation of peptides by high-performance liquid chromatography using predicted elution positions
-
Browne, C. A.; Bennett, H. P. J.; Solomon, S. The isolation of peptides by high-performance liquid chromatography using predicted elution positions Anal. Biochem. 1982, 124, 201-208
-
(1982)
Anal. Biochem.
, vol.124
, pp. 201-208
-
-
Browne, C.A.1
Bennett, H.P.J.2
Solomon, S.3
-
24
-
-
0032577264
-
Calculation of peptide retention coefficients in normal-phase liquid chromatography
-
DOI 10.1016/S0021-9673(98)00092-2, PII S0021967398000922
-
Yoshida, T. Calculation of peptide retention coefficients in normal-phase liquid chromatography J. Chromatogr., A 1998, 808, 105-112 (Pubitemid 28273224)
-
(1998)
Journal of Chromatography A
, vol.808
, Issue.1-2
, pp. 105-112
-
-
Yoshida, T.1
-
25
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte, J.; Doolittle, R. F. A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 1982, 157, 105-132
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
26
-
-
0014349825
-
The characterization of amino acid sequences in proteins by statistical methods
-
Zimmerman, J. M.; Eliezer, N.; Simha, R. The characterization of amino acid sequences in proteins by statistical methods J. Theor. Biol. 1968, 21, 170-201
-
(1968)
J. Theor. Biol.
, vol.21
, pp. 170-201
-
-
Zimmerman, J.M.1
Eliezer, N.2
Simha, R.3
-
27
-
-
0000929505
-
The hydrophobic moment detects periodicity in protein hydrophobicity
-
Eisenberg, D.; Weiss, R. M.; Terwilliger, T. C. The hydrophobic moment detects periodicity in protein hydrophobicity Proc. Natl. Acad. Sci. USA 1984, 81, 140-144 (Pubitemid 14180843)
-
(1984)
Proceedings of the National Academy of Sciences of the United States of America
, vol.81
, Issue.I1
, pp. 140-144
-
-
Eisenberg, D.1
Weiss, R.M.2
Terwilliger, T.C.3
-
29
-
-
77957378262
-
-
LIBSVM: a library for support vector machines;; software available at
-
Chang, C.-C.; Lin, C.-J. LIBSVM: a library for support vector machines; 2001; software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm.
-
(2001)
-
-
Chang, C.-C.1
Lin, C.-J.2
-
31
-
-
84950968334
-
Least median of squares regression
-
Rousseeuw, P. J. Least median of squares regression J. Am. Stat. Assoc. 1984, 79, 871-880
-
(1984)
J. Am. Stat. Assoc.
, vol.79
, pp. 871-880
-
-
Rousseeuw, P.J.1
-
32
-
-
33846706581
-
TOPP - The OpenMS proteomics pipeline
-
Kohlbacher, O.; Reinert, K.; Gropl, C.; Lange, E.; Pfeifer, N.; Schulz-Trieglaff, O.; Sturm, M. TOPP - the OpenMS proteomics pipeline Bioinformatics 2007, 23 e191-197
-
(2007)
Bioinformatics
, vol.23
-
-
Kohlbacher, O.1
Reinert, K.2
Gropl, C.3
Lange, E.4
Pfeifer, N.5
Schulz-Trieglaff, O.6
Sturm, M.7
-
33
-
-
77952075083
-
Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics
-
Bertsch, A.; Jung, S.; Zerck, A.; Pfeifer, N.; Nahnsen, S.; Henneges, C.; Nordheim, A.; Kohlbacher, O. Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics J. Proteome Res. 2010, 9, 2696-2704
-
(2010)
J. Proteome Res.
, vol.9
, pp. 2696-2704
-
-
Bertsch, A.1
Jung, S.2
Zerck, A.3
Pfeifer, N.4
Nahnsen, S.5
Henneges, C.6
Nordheim, A.7
Kohlbacher, O.8
-
34
-
-
26944481188
-
Interfaces and the driving force of hydrophobic assembly
-
Chandler, D. Interfaces and the driving force of hydrophobic assembly Nature 2005, 437, 640-647
-
(2005)
Nature
, vol.437
, pp. 640-647
-
-
Chandler, D.1
-
35
-
-
0031189914
-
Multitask learning
-
Caruana, R. Multitask learning Mach. Learn. 1997, 28, 41-75
-
(1997)
Mach. Learn.
, vol.28
, pp. 41-75
-
-
Caruana, R.1
|