-
1
-
-
33644966561
-
Effects of sequestration on signal transduction cascades
-
Blüthgen, N., Bruggeman, F. J., Legewie, S., Herzel, H., Westerhoff, H. V., and Kholodenko, B. N. (2006) Effects of sequestration on signal transduction cascades. Febs. J. 273, 895-906
-
(2006)
Febs. J.
, vol.273
, pp. 895-906
-
-
Blüthgen, N.1
Bruggeman, F.J.2
Legewie, S.3
Herzel, H.4
Westerhoff, H.V.5
Kholodenko, B.N.6
-
2
-
-
33846133955
-
Computational prediction of proteotypic peptides for quantitative proteomics
-
DOI 10.1038/nbt1275, PII NBT1275
-
Mallick, P., Schirle, M., Chen, S. S., Flory, M. R., Lee, H., Martin, D., Ranish, J., Raught, B., Schmitt, R., Werner, T., Kuster, B., and Aebersold, R. (2007) Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 25, 125-131 (Pubitemid 46098780)
-
(2007)
Nature Biotechnology
, vol.25
, Issue.1
, pp. 125-131
-
-
Mallick, P.1
Schirle, M.2
Chen, S.S.3
Flory, M.R.4
Lee, H.5
Martin, D.6
Ranish, J.7
Raught, B.8
Schmitt, R.9
Werner, T.10
Kuster, B.11
Aebersold, R.12
-
3
-
-
24044440791
-
Discovery of biomarker candidates within disease by protein profiling: Principles and concepts
-
DOI 10.1021/pr050122w
-
Marko-Varga, G., Lindberg, H., Löfdahl, C. G., Jönsson, P., Hansson, L., Dahlbäck, M., Lindquist, E., Johansson, L., Foster, M., and Fehniger, T. E. (2005) Discovery of biomarker candidates within disease by protein profiling: principles and concepts. J. Proteome Res. 4, 1200-1212 (Pubitemid 41213335)
-
(2005)
Journal of Proteome Research
, vol.4
, Issue.4
, pp. 1200-1212
-
-
Marko-Varga, G.1
Lindberg, H.2
Lofdahl, C.-G.3
Jonsson, P.4
Hansson, L.5
Dahlback, M.6
Lindquist, E.7
Johansson, L.8
Foster, M.9
Fehniger, T.E.10
-
4
-
-
39749171899
-
Application of targeted quantitative proteomics analysis in human cerebrospinal fluid using a liquid chromatography matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (LC MALDI TOF/TOF) platform
-
DOI 10.1021/pr700630x
-
Pan, S., Rush, J., Peskind, E. R., Galasko, D., Chung, K., Quinn, J., Jankovic, J., Leverenz, J. B., Zabetian, C., Pan, C., Wang, Y., Oh, J. H., Gao, J., Zhang, J., Montine, T., and Zhang, J. (2008) Application of Targeted Quantitative Proteomics Analysis in Human Cerebrospinal Fluid Using a Liquid Chromatography Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Tandem Mass Spectrometer (LC MALDI TOF/TOF) Platform. J. Proteome Res. 7, 720-730 (Pubitemid 351294034)
-
(2008)
Journal of Proteome Research
, vol.7
, Issue.2
, pp. 720-730
-
-
Pan, S.1
Rush, J.2
Peskind, E.R.3
Galasko, D.4
Chung, K.5
Quinn, J.6
Jankovic, J.7
Leverenz, J.B.8
Zabetian, C.9
Pan, C.10
Wang, Y.11
Jung, H.O.12
Gao, J.13
Zhang, J.14
Montine, T.15
Zhang, J.16
-
5
-
-
10244256354
-
Isotope dilution-mass spectrometric quantification of specific proteins: Model application with apolipoprotein A-I
-
Barr, J. R., Maggio, V. L., Patterson, D. G., Jr., Cooper, G. R., Henderson, L. O., Turner, W. E., Smith, S. J., Hannon, W. H., Needham, L. L., and Sampson, E. J. (1996) Isotope dilution-mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I. Clin. Chem. 42, 1676-1682 (Pubitemid 26354748)
-
(1996)
Clinical Chemistry
, vol.42
, Issue.10
, pp. 1676-1682
-
-
Barr, J.R.1
Maggio, V.L.2
Patterson Jr., D.G.3
Cooper, G.R.4
Henderson, L.O.5
Turner, W.E.6
Smith, S.J.7
Hannon, W.H.8
Needham, L.L.9
Sampson, E.J.10
-
6
-
-
23144442824
-
Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides
-
DOI 10.1038/nmeth774
-
Beynon, R. J., Doherty, M. K., Pratt, J. M., and Gaskell, S. J. (2005) Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Methods 2, 587-589 (Pubitemid 41086849)
-
(2005)
Nature Methods
, vol.2
, Issue.8
, pp. 587-589
-
-
Beynon, R.J.1
Doherty, M.K.2
Pratt, J.M.3
Gaskell, S.J.4
-
7
-
-
0037795741
-
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
-
DOI 10.1073/pnas.0832254100
-
Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., and Gygi, S. P. (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. U.S.A. 100, 6940-6945 (Pubitemid 36706372)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.12
, pp. 6940-6945
-
-
Gerber, S.A.1
Rush, J.2
Stemman, O.3
Kirschner, M.W.4
Gygi, S.P.5
-
8
-
-
68449102172
-
Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans
-
Malmström, J., Beck, M., Schmidt, A., Lange, V., Deutsch, E. W., and Aebersold, R. (2009) Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 460, 762-765
-
(2009)
Nature
, vol.460
, pp. 762-765
-
-
Malmström, J.1
Beck, M.2
Schmidt, A.3
Lange, V.4
Deutsch, E.W.5
Aebersold, R.6
-
9
-
-
33847179916
-
Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes
-
Pratt, J. M., Simpson, D. M., Doherty, M. K., Rivers, J., Gaskell, S. J., and Beynon, R. J. (2006) Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat. Protoc. 1, 1029-1043
-
(2006)
Nat. Protoc.
, vol.1
, pp. 1029-1043
-
-
Pratt, J.M.1
Simpson, D.M.2
Doherty, M.K.3
Rivers, J.4
Gaskell, S.J.5
Beynon, R.J.6
-
10
-
-
34548427053
-
Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT
-
DOI 10.1074/mcp.M600456-MCP200
-
Rivers, J., Simpson, D. M., Robertson, D. H., Gaskell, S. J., and Beynon, R. J. (2007) Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT. Mol. Cell. Proteomics 6, 1416-1427 (Pubitemid 47365439)
-
(2007)
Molecular and Cellular Proteomics
, vol.6
, Issue.8
, pp. 1416-1427
-
-
Rivers, J.1
Simpson, D.M.2
Robertson, D.H.L.3
Gaskell, S.J.4
Beynon, R.J.5
-
11
-
-
42649091860
-
Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics
-
DOI 10.1074/mcp.M700495-MCP200
-
Mirzaei, H., McBee, J. K., Watts, J., and Aebersold, R. (2008) Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Mol. Cell. Proteomics 7, 813-823 (Pubitemid 351597489)
-
(2008)
Molecular and Cellular Proteomics
, vol.7
, Issue.4
, pp. 813-823
-
-
Mirzaei, H.1
McBee, J.K.2
Watts, J.3
Aebersold, R.4
-
12
-
-
74049131716
-
High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
-
Picotti, P., Rinner, O., Stallmach, R., Dautel, F., Farrah, T., Domon, B., Wenschuh, H., and Aebersold, R. (2010) High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat. Methods 7, 43-46
-
(2010)
Nat. Methods
, vol.7
, pp. 43-46
-
-
Picotti, P.1
Rinner, O.2
Stallmach, R.3
Dautel, F.4
Farrah, T.5
Domon, B.6
Wenschuh, H.7
Aebersold, R.8
-
13
-
-
20544459800
-
Absolute quantification strategies in proteomics based on mass spectrometry
-
Brönstrup, M. (2004) Absolute quantification strategies in proteomics based on mass spectrometry. Expert Rev. Proteomics 1, 503-512
-
(2004)
Expert Rev. Proteomics
, vol.1
, pp. 503-512
-
-
Brönstrup, M.1
-
14
-
-
0037435030
-
Mass spectrometry-based proteomics
-
DOI 10.1038/nature01511
-
Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207 (Pubitemid 36362757)
-
(2003)
Nature
, vol.422
, Issue.6928
, pp. 198-207
-
-
Aebersold, R.1
Mann, M.2
-
15
-
-
84889414148
-
Influence of solvent composition and capillary temperature on the conformations of electrosprayed ions: Unfolding of compact ubiquitin conformers from pseudonative and denatured solutions
-
Li, J., Taraszka, J. A., Counterman, A. E., and Clemmer, D. E. (1999) Influence of solvent composition and capillary temperature on the conformations of electrosprayed ions: unfolding of compact ubiquitin conformers from pseudonative and denatured solutions. Int. J. Mass Spectrom. 185, 37-47
-
(1999)
Int. J. Mass Spectrom.
, vol.185
, pp. 37-47
-
-
Li, J.1
Taraszka, J.A.2
Counterman, A.E.3
Clemmer, D.E.4
-
16
-
-
0033214277
-
The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins
-
DOI 10.1021/ac990298f
-
Krause, E., Wenschuh, H., and Jungblut, P. R. (1999) The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins. Anal. Chem. 71, 4160-4165 (Pubitemid 29466391)
-
(1999)
Analytical Chemistry
, vol.71
, Issue.19
, pp. 4160-4165
-
-
Krause, E.1
Wenschuh, H.2
Jungblut, P.R.3
-
17
-
-
0036808751
-
Peptide mass fingerprinting peak intensity prediction: Extracting knowledge from spectra
-
DOI 10.1002/1615-9861(200210)2:10<1374::AID-PROT1374>3.0.CO;2-D
-
Gay, S., Binz, P. A., Hochstrasser, D. F., and Appel, R. D. (2002) Peptide mass fingerprinting peak intensity prediction: extracting knowledge from spectra. Proteomics 2, 1374-1391 (Pubitemid 35340019)
-
(2002)
Proteomics
, vol.2
, Issue.10
, pp. 1374-1391
-
-
Gay, S.1
Binz, P.-A.2
Hochstrasser, D.F.3
Appel, R.D.4
-
18
-
-
38349172005
-
Prediction of peptides observable by mass spectrometry applied at the experimental set level
-
Sanders, W. S., Bridges, S. M., McCarthy, F. M., Nanduri, B., and Burgess, S. C. (2007) Prediction of peptides observable by mass spectrometry applied at the experimental set level. BMC Bioinformatics 8, S23
-
(2007)
BMC Bioinformatics
, vol.8
-
-
Sanders, W.S.1
Bridges, S.M.2
McCarthy, F.M.3
Nanduri, B.4
Burgess, S.C.5
-
19
-
-
21744435622
-
Scoring proteomes with proteotypic peptide probes
-
DOI 10.1038/nrm1683
-
Kuster, B., Schirle, M., Mallick, P., and Aebersold, R. (2005) Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol. 6, 577-583 (Pubitemid 40943048)
-
(2005)
Nature Reviews Molecular Cell Biology
, vol.6
, Issue.7
, pp. 577-583
-
-
Kuster, B.1
Schirle, M.2
Mallick, P.3
Aebersold, R.4
-
20
-
-
59849093889
-
Prediction of high-responding peptides for targeted protein assays by mass spectrometry
-
Fusaro, V. A., Mani, D. R., Mesirov, J. P., and Carr, S. A. (2009) Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat. Biotechnol. 27, 190-198
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 190-198
-
-
Fusaro, V.A.1
Mani, D.R.2
Mesirov, J.P.3
Carr, S.A.4
-
21
-
-
43049127826
-
PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows
-
DOI 10.1038/embor.2008.56, PII EMBOR200856
-
Deutsch, E. W., Lam, H., and Aebersold, R. (2008) PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 9, 429-434 (Pubitemid 351627279)
-
(2008)
EMBO Reports
, vol.9
, Issue.5
, pp. 429-434
-
-
Deutsch, E.W.1
Lam, H.2
Aebersold, R.3
-
22
-
-
33846632267
-
Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics
-
DOI 10.1021/pr060507u
-
Siepen, J. A., Keevil, E. J., Knight, D., and Hubbard, S. J. (2007) Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics. J. Proteome Res. 6, 399-408 (Pubitemid 46173693)
-
(2007)
Journal of Proteome Research
, vol.6
, Issue.1
, pp. 399-408
-
-
Siepen, J.A.1
Keevil, E.-J.2
Knight, D.3
Hubbard, S.J.4
-
23
-
-
0037108887
-
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
-
DOI 10.1021/ac025747h
-
Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392 (Pubitemid 35215372)
-
(2002)
Analytical Chemistry
, vol.74
, Issue.20
, pp. 5383-5392
-
-
Keller, A.1
Nesvizhskii, A.I.2
Kolker, E.3
Aebersold, R.4
-
24
-
-
38549155006
-
AAindex: Amino acid index database, progress report 2008
-
DOI 10.1093/nar/gkm998
-
Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T., and Kanehisa, M. (2008) AAindex: amino acid index database, progress report 2008. Nucleic Acids Res. 36, D202-205 (Pubitemid 351149722)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Kawashima, S.1
Pokarowski, P.2
Pokarowska, M.3
Kolinski, A.4
Katayama, T.5
Kanehisa, M.6
-
25
-
-
0028289435
-
Determination of free energies of N-capping in alpha-helices by modification of the Lifson-Roig helix-coil theory to include N- and C-capping
-
Doig, A. J., Chakrabartty, A., Klingler, T. M., and Baldwin, R. L. (1994) Determination of free energies of N-capping in alpha-helices by modification of the Lifson-Roig helix-coil therapy to include N- and C-capping. Biochemistry 33, 3396-3403 (Pubitemid 24112654)
-
(1994)
Biochemistry
, vol.33
, Issue.11
, pp. 3396-3403
-
-
Doig, A.J.1
Chakrabartty, A.2
Klingler, T.M.3
Baldwin, R.L.4
-
26
-
-
34249753618
-
SUPPORT-VECTOR NETWORKS
-
Cortes, C., and Vapnik, V. (1995) SUPPORT-VECTOR NETWORKS. Machine Learning 20, 273-297
-
(1995)
Machine Learning
, vol.20
, pp. 273-297
-
-
Cortes, C.1
Vapnik, V.2
-
27
-
-
55449125185
-
Support Vector Machines and Kernels for Computational Biology
-
Ben-Hur, A., Ong, C. S., Sonnenburg, S. R., Schölkopf, B., and Rätsch, G. (2008) Support Vector Machines and Kernels for Computational Biology. PLoS Comput. Biol. 4, e1000173
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Ben-Hur, A.1
Ong, C.S.2
Sonnenburg, S.R.3
Schölkopf, B.4
Rätsch, G.5
-
28
-
-
0001938951
-
Transductive inference for text classification using Support Vector Machines
-
Bratko, I., and Dzeroski, S., eds. Morgan Kaufmann Pub Inc, San Francisco
-
Joachims, T. (1999) Transductive inference for text classification using Support Vector Machines. In: Bratko, I., and Dzeroski, S., eds. Machine Learning, Proceedings, pp. 200-209, Morgan Kaufmann Pub Inc, San Francisco
-
(1999)
Machine Learning, Proceedings
, pp. 200-209
-
-
Joachims, T.1
-
29
-
-
0035478854
-
Random forests
-
Breiman, L. (2001) Random forests. Machine Learning 45, 5-32
-
(2001)
Machine Learning
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
31
-
-
84887828724
-
Peptide detectability prediction following ESI mass spectrometry using genetic programming
-
Wedge, D., Lau, K. W., Gaskell, S. J., Hubbard, S. J., Kell, D. B., and Eyers, C. E. (2007) Peptide detectability prediction following ESI mass spectrometry using genetic programming. GECCO 2007: Proceedings of the 9th annual conference on Genetic and Evolutionary Computation
-
(2007)
GECCO 2007: Proceedings of the 9th Annual Conference on Genetic and Evolutionary Computation
-
-
Wedge, D.1
Lau, K.W.2
Gaskell, S.J.3
Hubbard, S.J.4
Kell, D.B.5
Eyers, C.E.6
-
34
-
-
0000169232
-
An algorithm for least-squares estimation of nonlinear parameters
-
Marquardt, D. W. (1963) An algorithm for least-squares estimation of nonlinear parameters. J. Soc. Industr. Appl. Math. 11, 431-441
-
(1963)
J. Soc. Industr. Appl. Math.
, vol.11
, pp. 431-441
-
-
Marquardt, D.W.1
-
36
-
-
33747885134
-
A computational approach toward label-free protein quantification using predicted peptide detectability
-
DOI 10.1093/bioinformatics/btl237
-
Tang, H., Arnold, R. J., Alves, P., Xun, Z., Clemmer, D. E., Novotny, M. V., Reilly, J. P., and Radivojac, P. (2006) A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics 22, e481-488 (Pubitemid 44288319)
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Tang, H.1
Arnold, R.J.2
Alves, P.3
Xun, Z.4
Clemmer, D.E.5
Novotny, M.V.6
Reilly, J.P.7
Radivojac, P.8
-
37
-
-
77954210153
-
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
-
Webb-Robertson, B. J., Cannon, W. R., Oehmen, C. S., Shah, A. R., Gurumoorthi, V., Lipton, M. S., and Waters, K. M. (2010) A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics. Bioinformatics 26, 1677-1683
-
(2010)
Bioinformatics
, vol.26
, pp. 1677-1683
-
-
Webb-Robertson, B.J.1
Cannon, W.R.2
Oehmen, C.S.3
Shah, A.R.4
Gurumoorthi, V.5
Lipton, M.S.6
Waters, K.M.7
-
38
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T. L. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10, 421
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
39
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
40
-
-
0031930082
-
The ease of peptide detection by matrix-assisted laser desorption/ionization mass spectrometry: The effect of secondary structure on signal intensity
-
DOI 10.1002/(SICI)1097-0231(19980214)12:3<115::AID-RCM124>3.0.CO;2- 5
-
Wenschuh, H., Halada, P., Lamer, S., Jungblut, P., and Krause, E. (1998) The ease of peptide detection by matrix-assisted laser desorption/ionization mass spectrometry: the effect of secondary structure on signal intensity. Rapid Commun. Mass Spectrom. 12, 115-119 (Pubitemid 28073308)
-
(1998)
Rapid Communications in Mass Spectrometry
, vol.12
, Issue.3
, pp. 115-119
-
-
Wenschuh, H.1
Halada, P.2
Lamer, S.3
Jungblut, P.4
Krause, E.5
-
41
-
-
69549121810
-
The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions
-
Tao, L., Dahl, D. B., Pérez, L. M., and Russell, D. H. (2009) The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions. J. Am. Soc. Mass Spectrom. 20, 1593-1602
-
(2009)
J. Am. Soc. Mass Spectrom.
, vol.20
, pp. 1593-1602
-
-
Tao, L.1
Dahl, D.B.2
Pérez, L.M.3
Russell, D.H.4
-
42
-
-
0026058806
-
Physical reasons for secondary structure stability: Alpha-helices in short peptides
-
Finkelstein, A. V., Badretdinov, A. Y., and Ptitsyn, O. B. (1991) Physical reasons for secondary structure stability: alpha-helices in short peptides. Proteins 10, 287-299
-
(1991)
Proteins
, vol.10
, pp. 287-299
-
-
Finkelstein, A.V.1
Badretdinov, A.Y.2
Ptitsyn, O.B.3
-
43
-
-
0023192524
-
Peptide quantitative structure-activity relationships, a multivariate approach
-
Hellberg, S., Sjöstrom, M., Skagerberg, B., and Wold, S. (1987) Peptide quantitative structure-activity relationships, a multivariate approach. J. Med. Chem. 30, 1126-1135 (Pubitemid 17117970)
-
(1987)
Journal of Medicinal Chemistry
, vol.30
, Issue.7
, pp. 1126-1135
-
-
Hellberg, S.1
Sjostrom, M.2
Skagerberg, B.3
Wold, S.4
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