-
1
-
-
9244226546
-
Design and analysis of experiments with high throughput biological assay data
-
Rocke DM. Design and analysis of experiments with high throughput biological assay data. Semin Cell Dev Biol 2004; 15:703-13.
-
(2004)
Semin Cell Dev Biol
, vol.15
, pp. 703-713
-
-
Rocke, D.M.1
-
2
-
-
33750601062
-
The pitfalls of proteomics experiments without the correct use of bioinformatics tools
-
Biron DG, Brun C, Lefevre T, et al. The pitfalls of proteomics experiments without the correct use of bioinformatics tools. Proteomics 2006;6:5577-96.
-
(2006)
Proteomics
, vol.6
, pp. 5577-5596
-
-
Biron, D.G.1
Brun, C.2
Lefevre, T.3
-
3
-
-
33750600611
-
Proteome informatics I: Bioinformatics tools for processing experimental data
-
Palagi PM, Hernandez P, Walther D, et al. Proteome informatics I: bioinformatics tools for processing experimental data. Proteomics 2006;6:5435-44.
-
(2006)
Proteomics
, vol.6
, pp. 5435-5444
-
-
Palagi, P.M.1
Hernandez, P.2
Walther, D.3
-
4
-
-
10644230916
-
Current two-dimensional electrophoresis technology for proteomics
-
Gorg A, Weiss W, Dunn MJ. Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004; 4:3665-85.
-
(2004)
Proteomics
, vol.4
, pp. 3665-3685
-
-
Gorg, A.1
Weiss, W.2
Dunn, M.J.3
-
5
-
-
0037435030
-
Mass spectrometry-based proteomics
-
Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 2003;422:198-207.
-
(2003)
Nature
, vol.422
, pp. 198-207
-
-
Aebersold, R.1
Mann, M.2
-
6
-
-
3042735127
-
The need for guidelines in publication of peptide and protein identification data
-
Carr S, Aebersold R, Baldwin M, et al. The need for guidelines in publication of peptide and protein identification data. Mol Cell Proteomics 2004;3:531-3.
-
(2004)
Mol Cell Proteomics
, vol.3
, pp. 531-533
-
-
Carr, S.1
Aebersold, R.2
Baldwin, M.3
-
7
-
-
27744477157
-
Bridging proteomics and systems biology what are the roads to be traveled?
-
Souchelnytskyi S. Bridging proteomics and systems biology what are the roads to be traveled? Proteomics 2005; 5:4123-37.
-
(2005)
Proteomics
, vol.5
, pp. 4123-4137
-
-
Souchelnytskyi, S.1
-
8
-
-
35848968214
-
The protein microscope: Incorporating mass spectrometry into cell biology
-
Bell AW, Nilsson T, Kearney RE, et al. The protein microscope: incorporating mass spectrometry into cell biology. Nat Methods 2007;4:783-4.
-
(2007)
Nat Methods
, vol.4
, pp. 783-784
-
-
Bell, A.W.1
Nilsson, T.2
Kearney, R.E.3
-
9
-
-
33745978799
-
Evaluation of two sample preparation methods for prostate proteome analysis
-
Lexander H, Hellman U, Palmberg C, et al. Evaluation of two sample preparation methods for prostate proteome analysis. Proteomics 2006;6:3918-25.
-
(2006)
Proteomics
, vol.6
, pp. 3918-3925
-
-
Lexander, H.1
Hellman, U.2
Palmberg, C.3
-
10
-
-
30744440918
-
Systematic evaluation of sample preparation methods for gel-based human urinary proteomics: Quantity, quality, and variability
-
Thongboonkerd V, Chutipongtanate S, Kanlaya R. Systematic evaluation of sample preparation methods for gel-based human urinary proteomics: quantity, quality, and variability. J Proteome Res 2006;5 183-91.
-
(2006)
J Proteome Res
, vol.5
, pp. 183-191
-
-
Thongboonkerd, V.1
Chutipongtanate, S.2
Kanlaya, R.3
-
11
-
-
33846464622
-
A standard operating procedure (SOP) for the preparation of intra- and extracellular proteins of Clostridium acetobutylicum for proteome analysis
-
Schwarz K, Fiedler T, Fischer RJ, et al. A standard operating procedure (SOP) for the preparation of intra- and extracellular proteins of Clostridium acetobutylicum for proteome analysis. J Microbiol Methods 2007;68:396-402.
-
(2007)
J Microbiol Methods
, vol.68
, pp. 396-402
-
-
Schwarz, K.1
Fiedler, T.2
Fischer, R.J.3
-
12
-
-
20844446602
-
Optimal replication and the importance of experimental design for gel-based quantitative proteomics
-
Hunt SM, Thomas MR, Sebastian LT, et al. Optimal replication and the importance of experimental design for gel-based quantitative proteomics. J Proteome Res 2005;4: 809-19.
-
(2005)
J Proteome Res
, vol.4
, pp. 809-819
-
-
Hunt, S.M.1
Thomas, M.R.2
Sebastian, L.T.3
-
13
-
-
26844438450
-
Impact of replicate types on proteomics expression analysis
-
Karp NA, Spencer M, Lindsay H, et al. Impact of replicate types on proteomics expression analysis. J Proteome Res 2005; 4 1867-71.
-
(2005)
J Proteome Res
, vol.4
, pp. 1867-1871
-
-
Karp, N.A.1
Spencer, M.2
Lindsay, H.3
-
14
-
-
0023768475
-
The current state of two-dimensional electrophoresis with immobilized pH gradients
-
Gorg A, Postel W, Gunther S. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 1988;9:531-46.
-
(1988)
Electrophoresis
, vol.9
, pp. 531-546
-
-
Gorg, A.1
Postel, W.2
Gunther, S.3
-
15
-
-
3543118467
-
Proteomic response to amino acid starvation in Candida albicans and Saccharomyces cerevisiae
-
Yin Z, Stead D, Selway L, et al. Proteomic response to amino acid starvation in Candida albicans and Saccharomyces cerevisiae. Proteomics 2004;4:2425-36.
-
(2004)
Proteomics
, vol.4
, pp. 2425-2436
-
-
Yin, Z.1
Stead, D.2
Selway, L.3
-
16
-
-
39049191688
-
Quantitative analysis of 2D gels
-
Zivy M. Quantitative analysis of 2D gels. Methods Mol Biol 2007; 355:175-94.
-
(2007)
Methods Mol Biol
, vol.355
, pp. 175-194
-
-
Zivy, M.1
-
17
-
-
23844491490
-
Maximising sensitivity for detecting changes in protein expression: Experimental design using minimal CyDyes
-
Karp NA, Lilley KS. Maximising sensitivity for detecting changes in protein expression: Experimental design using minimal CyDyes. Proteomics 2005;5:3105-15.
-
(2005)
Proteomics
, vol.5
, pp. 3105-3115
-
-
Karp, N.A.1
Lilley, K.S.2
-
18
-
-
32244443103
-
Multivariate statistical tools applied to the characterization of the proteomic profiles of two human lymphoma cell lines by two-dimensional gel electrophoresis
-
Marengo E, Robotti E, Bobba M, et al. Multivariate statistical tools applied to the characterization of the proteomic profiles of two human lymphoma cell lines by two-dimensional gel electrophoresis. Electrophoresis 2006;27: 484-94.
-
(2006)
Electrophoresis
, vol.27
, pp. 484-494
-
-
Marengo, E.1
Robotti, E.2
Bobba, M.3
-
20
-
-
16344384887
-
The importance of experimental design in proteomic mass spectrometry experiments: Some cautionary tales
-
Hu J, Coombes KR, Morris JS, et al. The importance of experimental design in proteomic mass spectrometry experiments: Some cautionary tales. Brief Funct Genomic Proteomic 2005;3:322-31.
-
(2005)
Brief Funct Genomic Proteomic
, vol.3
, pp. 322-331
-
-
Hu, J.1
Coombes, K.R.2
Morris, J.S.3
-
21
-
-
0041884952
-
Identification of 2D-gel proteins: A comparison of MALDI/TOF peptide mass mapping to μ LC-ESI tandem mass spectrometry
-
Lim H, Eng J, Yates JR 3rd, et al. Identification of 2D-gel proteins: A comparison of MALDI/TOF peptide mass mapping to μ LC-ESI tandem mass spectrometry. J Am Soc Mass Spectrom 2003;14 957-70.
-
(2003)
J Am Soc Mass Spectrom
, vol.14
, pp. 957-970
-
-
Lim, H.1
Eng, J.2
Yates 3rd, J.R.3
-
22
-
-
33746302310
-
Universal metrics for quality assessment of protein identifications by mass spectrometry
-
Stead DA, Preece A, Brown AJP. Universal metrics for quality assessment of protein identifications by mass spectrometry. Mol Cell Proteomics 2006;5:1205-11.
-
(2006)
Mol Cell Proteomics
, vol.5
, pp. 1205-1211
-
-
Stead, D.A.1
Preece, A.2
Brown, A.J.P.3
-
23
-
-
42049116382
-
-
Aldente. http://ca.expasy.org/tools/aldente/ (7 January 2008, date last accessed).
-
Aldente. http://ca.expasy.org/tools/aldente/ (7 January 2008, date last accessed).
-
-
-
-
24
-
-
33644925149
-
Aldente and BioGraph: An improved peptide mass fingerprinting protein identification environment
-
December, Ed. FontisMedia ISBN 2-88476-004-0
-
Tuloup M, Hernandez C, Coro I, et al. Aldente and BioGraph: An improved peptide mass fingerprinting protein identification environment. Swiss Proteomics Society 2003 Congress: Understanding Biological Systems through Proteomics, Basel, Switzerland, 2-4 December, 2003, Ed. FontisMedia (ISBN 2-88476-004-0), 174-176.
-
(2003)
Swiss Proteomics Society 2003 Congress: Understanding Biological Systems through Proteomics, Basel, Switzerland, 2-4
, pp. 174-176
-
-
Tuloup, M.1
Hernandez, C.2
Coro, I.3
-
25
-
-
42049097079
-
-
Mascot. http://www.matrixscience.com/search_forrm_select.html/ (7 January 2008, date last accessed).
-
Mascot. http://www.matrixscience.com/search_forrm_select.html/ (7 January 2008, date last accessed).
-
-
-
-
26
-
-
42049086161
-
-
ProFound. http://prowl.rockefeller.edu/prowl-cgi/profound.exe/ (7 January 2008, date last accessed).
-
ProFound. http://prowl.rockefeller.edu/prowl-cgi/profound.exe/ (7 January 2008, date last accessed).
-
-
-
-
27
-
-
1542720811
-
Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data
-
Chamrad DC, Korting G, Stuhler K, et al. Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data. Proteomics 2004;4: 619-28.
-
(2004)
Proteomics
, vol.4
, pp. 619-628
-
-
Chamrad, D.C.1
Korting, G.2
Stuhler, K.3
-
29
-
-
39049175370
-
Protein identification by tandem mass spectrometry and sequence database searching
-
Nesvizhskii AI. Protein identification by tandem mass spectrometry and sequence database searching. Methods Mol Biol 2007;367 87-119.
-
(2007)
Methods Mol Biol
, vol.367
, pp. 87-119
-
-
Nesvizhskii, A.I.1
-
30
-
-
0028575316
-
Error-tolerant identification of peptides in sequence databases by peptide sequence tags
-
Mann M, Wilm M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem 1994;66:4390-9.
-
(1994)
Anal Chem
, vol.66
, pp. 4390-4399
-
-
Mann, M.1
Wilm, M.2
-
31
-
-
42049100616
-
-
SEQUEST. http://fields.scripps.edu/sequest/ (7 January 2008, date last accessed).
-
SEQUEST. http://fields.scripps.edu/sequest/ (7 January 2008, date last accessed).
-
-
-
-
32
-
-
15744400109
-
Comparison of different search engines using validated MS/MS test datasets
-
Boutilier K, Ross M, Podtelejnikov AV, et al. Comparison of different search engines using validated MS/MS test datasets. Anal Chim Acta 2005;534:11-20.
-
(2005)
Anal Chim Acta
, vol.534
, pp. 11-20
-
-
Boutilier, K.1
Ross, M.2
Podtelejnikov, A.V.3
-
33
-
-
23944451618
-
An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS seareh algorithms: Sensitivity and specificity analysis
-
Kapp EA, Schutz F, Connolly LM, et al. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS seareh algorithms: Sensitivity and specificity analysis. Proteomics 2005;5:3475-90.
-
(2005)
Proteomics
, vol.5
, pp. 3475-3490
-
-
Kapp, E.A.1
Schutz, F.2
Connolly, L.M.3
-
34
-
-
42049116381
-
-
Phenyx main site. http://www.phenyx-ms.com/ (7 January 2008, date last accessed).
-
Phenyx main site. http://www.phenyx-ms.com/ (7 January 2008, date last accessed).
-
-
-
-
35
-
-
42049114525
-
-
Phenyx public server. http://phenyx.vital-it.ch/pwi/ (7 January 2008, date last accessed).
-
Phenyx public server. http://phenyx.vital-it.ch/pwi/ (7 January 2008, date last accessed).
-
-
-
-
36
-
-
42049088797
-
-
OMSSA. http://pubchem.ncbi.nlm.nih.gov/omssa/ (7 January 2008, date last accessed).
-
OMSSA. http://pubchem.ncbi.nlm.nih.gov/omssa/ (7 January 2008, date last accessed).
-
-
-
-
37
-
-
42049123302
-
-
X! Tandem. http://www.thegpm.org/TANDEM/index.html/ (7 January 2008, date last accessed).
-
X! Tandem. http://www.thegpm.org/TANDEM/index.html/ (7 January 2008, date last accessed).
-
-
-
-
38
-
-
39049191583
-
Proteomic data exchange and storage: The need for common standards and public repositories
-
Orchard S, Jones P, Taylor C, et al. Proteomic data exchange and storage: The need for common standards and public repositories. Methods Mol Biol 2007;367:261-70.
-
(2007)
Methods Mol Biol
, vol.367
, pp. 261-270
-
-
Orchard, S.1
Jones, P.2
Taylor, C.3
-
39
-
-
24744455665
-
Automatic quality assessment of peptide tandem mass spectra
-
Bern M, Goldberg D, McDonald WH, et al. Automatic quality assessment of peptide tandem mass spectra. Bioinformatics 2004; 20(Suppl 1):I49-54.
-
(2004)
Bioinformatics
, vol.20
, Issue.SUPPL. 1
-
-
Bern, M.1
Goldberg, D.2
McDonald, W.H.3
-
40
-
-
33645653958
-
Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering
-
Flikka K, Martens L, Vandekerckhove J, et al. Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering. Proteomics 2006;6: 2086-94.
-
(2006)
Proteomics
, vol.6
, pp. 2086-2094
-
-
Flikka, K.1
Martens, L.2
Vandekerckhove, J.3
-
41
-
-
33645708138
-
Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: Toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides
-
Nesvizhskii AI, Roos FF, Grossmann J, et al. Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: Toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteomics 2006;5:652-70.
-
(2006)
Mol Cell Proteomics
, vol.5
, pp. 652-670
-
-
Nesvizhskii, A.I.1
Roos, F.F.2
Grossmann, J.3
-
42
-
-
33847654762
-
msmsEval: Tandem mass spectral quality assignment for high-throughput proteomics
-
Wong JW, Sullivan MJ, Cartwright HM, et al. msmsEval: Tandem mass spectral quality assignment for high-throughput proteomics. BMC Bioinformatics 2007;8:51.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 51
-
-
Wong, J.W.1
Sullivan, M.J.2
Cartwright, H.M.3
-
43
-
-
33645467062
-
Improved classification of mass spectrometry database search results using newer machine learning approaches
-
Ulintz PJ, Zhu J, Qin ZS, et al. Improved classification of mass spectrometry database search results using newer machine learning approaches. Mol Cell Proteomics 2006;5:497-509.
-
(2006)
Mol Cell Proteomics
, vol.5
, pp. 497-509
-
-
Ulintz, P.J.1
Zhu, J.2
Qin, Z.S.3
-
44
-
-
27944488300
-
Confident protein identification using like average peptide score method coupled with search-specific, ab initio thresholds
-
Shadforth I, Dunkley T, Lilley K, et al. Confident protein identification using like average peptide score method coupled with search-specific, ab initio thresholds. Rapid Commun Mass Spectrom 2005;19:3363-8.
-
(2005)
Rapid Commun Mass Spectrom
, vol.19
, pp. 3363-3368
-
-
Shadforth, I.1
Dunkley, T.2
Lilley, K.3
-
45
-
-
24044508863
-
New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques
-
Savitski MM, Nielsen ML, Zubarev RA. New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques. Mol Cell Proteomics 2005; 4 1180-8.
-
(2005)
Mol Cell Proteomics
, vol.4
, pp. 1180-1188
-
-
Savitski, M.M.1
Nielsen, M.L.2
Zubarev, R.A.3
-
46
-
-
33745828376
-
Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profiles
-
Piening BD, Wang P, Bangur CS, et al. Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profiles. J Proteome Res 2006;5:1527-34.
-
(2006)
J Proteome Res
, vol.5
, pp. 1527-1534
-
-
Piening, B.D.1
Wang, P.2
Bangur, C.S.3
-
47
-
-
42049122886
-
-
Global Proteome Machine. http://gpmdb.thegpm.org/ (7 January 2008, date last accessed).
-
Global Proteome Machine. http://gpmdb.thegpm.org/ (7 January 2008, date last accessed).
-
-
-
-
48
-
-
42049084043
-
-
PeptideAtlas. http://www.peptideatlas.org/ (7 January 2008, date last accessed).
-
PeptideAtlas. http://www.peptideatlas.org/ (7 January 2008, date last accessed).
-
-
-
-
50
-
-
34548802987
-
Probability-based pattern recognition and statistical framework for randomization: Modeling tandem mass spectrum/ peptide sequence false match frequencies
-
Feng J, Naiman DQ, Cooper B. Probability-based pattern recognition and statistical framework for randomization: Modeling tandem mass spectrum/ peptide sequence false match frequencies. Bioinformatics 2007; 23:2210-7.
-
(2007)
Bioinformatics
, vol.23
, pp. 2210-2217
-
-
Feng, J.1
Naiman, D.Q.2
Cooper, B.3
-
51
-
-
34249316472
-
Estimating the statistical significance of peptide identifications from shotgun proteomics experiments
-
Higgs RE, Knierman MD, Freeman AB, et al. Estimating the statistical significance of peptide identifications from shotgun proteomics experiments. J Proteome Res 2007;6: 1758-67.
-
(2007)
J Proteome Res
, vol.6
, pp. 1758-1767
-
-
Higgs, R.E.1
Knierman, M.D.2
Freeman, A.B.3
-
52
-
-
33846567441
-
Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy
-
Huttlin EL, Hegeman AD, Harms AC, et al. Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy. J Proteome Res 2007;6:392-8.
-
(2007)
J Proteome Res
, vol.6
, pp. 392-398
-
-
Huttlin, E.L.1
Hegeman, A.D.2
Harms, A.C.3
-
54
-
-
33644524918
-
Mass spectrometry-based proteomics turns quantitative
-
Ong SE, Mann M. Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol 2005;1:252-62.
-
(2005)
Nat Chem Biol
, vol.1
, pp. 252-262
-
-
Ong, S.E.1
Mann, M.2
-
55
-
-
19444363756
-
Mass spectrometry-based quantitative proteomic profiling
-
Yan W, Chen SS. Mass spectrometry-based quantitative proteomic profiling. Brief Funct Genomic Proteomic 2005;4: 27-38.
-
(2005)
Brief Funct Genomic Proteomic
, vol.4
, pp. 27-38
-
-
Yan, W.1
Chen, S.S.2
-
56
-
-
33846926966
-
Amino acid-coded tagging approaches in quantitative proteomics
-
Chen X, Sun L, Yu Y, et al. Amino acid-coded tagging approaches in quantitative proteomics. Expert Rev Proteomics 2007;4:25-37.
-
(2007)
Expert Rev Proteomics
, vol.4
, pp. 25-37
-
-
Chen, X.1
Sun, L.2
Yu, Y.3
-
57
-
-
0036583926
-
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
-
Ong SE, Blagoev B, Kratchmarova I, et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Gell Proteomics 2002;1:376-86.
-
(2002)
Mol Gell Proteomics
, vol.1
, pp. 376-386
-
-
Ong, S.E.1
Blagoev, B.2
Kratchmarova, I.3
-
58
-
-
13244260803
-
A novel strategy for quantitative proteomics using isotope-coded protein labels
-
Schmidt A, Kellermann J, Lottspeich F. A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 2005; 5:4-15.
-
(2005)
Proteomics
, vol.5
, pp. 4-15
-
-
Schmidt, A.1
Kellermann, J.2
Lottspeich, F.3
-
59
-
-
19944432197
-
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
-
Ross PL, Huang YN, Marchese JN, et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004;3:1154-69.
-
(2004)
Mol Cell Proteomics
, vol.3
, pp. 1154-1169
-
-
Ross, P.L.1
Huang, Y.N.2
Marchese, J.N.3
-
61
-
-
20644442887
-
MSight: An image analysis software for liquid chromatography-mass spectrometry
-
Palagi PM, Walther D, Quadroni M, et al. MSight: An image analysis software for liquid chromatography-mass spectrometry. Proteomics 2005;5:2381-4.
-
(2005)
Proteomics
, vol.5
, pp. 2381-2384
-
-
Palagi, P.M.1
Walther, D.2
Quadroni, M.3
-
62
-
-
42049085346
-
-
MSight. http://www.expasy.org/MSight/ (7 January 2008, date last accessed).
-
MSight. http://www.expasy.org/MSight/ (7 January 2008, date last accessed).
-
-
-
-
63
-
-
33947434519
-
Automated reporting from gel-based proteomics experiments using the open source Proteios database application
-
Levander F, Krogh M, Warell K, et al. Automated reporting from gel-based proteomics experiments using the open source Proteios database application. Proteomics 2007;7: 668-74.
-
(2007)
Proteomics
, vol.7
, pp. 668-674
-
-
Levander, F.1
Krogh, M.2
Warell, K.3
-
64
-
-
33750601225
-
Proteome informatics II: Bioinformatics for comparative proteomics
-
Lisacek F, Cohen-Boulakia S, Appel RD. Proteome informatics II: bioinformatics for comparative proteomics. Proteomics 2006;6 5445-66.
-
(2006)
Proteomics
, vol.6
, pp. 5445-5466
-
-
Lisacek, F.1
Cohen-Boulakia, S.2
Appel, R.D.3
-
65
-
-
42049110209
-
-
Trans-Proteomic Pipeline. http://tools.proteomecenter.org/software.php/ (7 January 2008, date last accessed).
-
Trans-Proteomic Pipeline. http://tools.proteomecenter.org/software.php/ (7 January 2008, date last accessed).
-
-
-
-
66
-
-
33746930864
-
-
Keller A, Eng J, Zhang N, Li XJ. Aebersold R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol 2005;1:2005.0017 [Epub 2005 Aug 2].
-
Keller A, Eng J, Zhang N, Li XJ. Aebersold R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol 2005;1:2005.0017 [Epub 2005 Aug 2].
-
-
-
-
67
-
-
42049084247
-
-
Proteome Standards Initiative. http://www.psidev.info/ (7 January 2008, date last accessed).
-
Proteome Standards Initiative. http://www.psidev.info/ (7 January 2008, date last accessed).
-
-
-
-
68
-
-
42049094713
-
-
Human Proteome Organisation. http://www.hupo.org/ (7 January 2008, date last accessed).
-
Human Proteome Organisation. http://www.hupo.org/ (7 January 2008, date last accessed).
-
-
-
-
69
-
-
33750285086
-
The HUPO proteomics standards initiative - overcoming the fragmentation of proteomics data
-
Hermjakob U. The HUPO proteomics standards initiative - overcoming the fragmentation of proteomics data. Proteomics 2006;6:34-8.
-
(2006)
Proteomics
, vol.6
, pp. 34-38
-
-
Hermjakob, U.1
-
70
-
-
34249062964
-
The minimum information about a proteomics: Experiment (MIAPE)
-
Taylor CF, Paton NW, Lilley KS, et al. The minimum information about a proteomics: Experiment (MIAPE). Nat Biotechnol 2007;25 887-93.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 887-893
-
-
Taylor, C.F.1
Paton, N.W.2
Lilley, K.S.3
-
71
-
-
0742323374
-
The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data
-
Hermjakob H, Montecchi-Palazzi L, Bader G, et al. The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data. Nat Biotechnol 2004;22:177-83.
-
(2004)
Nat Biotechnol
, vol.22
, pp. 177-183
-
-
Hermjakob, H.1
Montecchi-Palazzi, L.2
Bader, G.3
-
72
-
-
0037337307
-
A systematic approach to modeling, capturing, and disseminating proteomics experimental data
-
Taylor CF, Paton NW, Garwood KL, et al. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol 2003;21: 247-54.
-
(2003)
Nat Biotechnol
, vol.21
, pp. 247-254
-
-
Taylor, C.F.1
Paton, N.W.2
Garwood, K.L.3
-
73
-
-
8344284323
-
A common open representation of mass spectrometry data and its application to proteomics research
-
Pedrioli PG, Eng JK, Hubley R, et al. A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 2004;22: 1459-66.
-
(2004)
Nat Biotechnol
, vol.22
, pp. 1459-1466
-
-
Pedrioli, P.G.1
Eng, J.K.2
Hubley, R.3
-
74
-
-
9144233086
-
PEDRo: A database for storing, searching and disseminating experimental proteomics data
-
Garwood K, McLaughlin T, Garwood C, et al. PEDRo: A database for storing, searching and disseminating experimental proteomics data. BMC Genomics 2004;5: 68.
-
(2004)
BMC Genomics
, vol.5
, pp. 68
-
-
Garwood, K.1
McLaughlin, T.2
Garwood, C.3
-
75
-
-
42049092194
-
-
PRIDE. http://www.ebi.ac.uk/pride/ (7 January 2008, date last accessed).
-
PRIDE. http://www.ebi.ac.uk/pride/ (7 January 2008, date last accessed).
-
-
-
-
76
-
-
42049087705
-
-
Open Proteomics Database. http://bioinformatics.icmb.utexas.edu/OPD/ (7 January 2008, date last accessed).
-
Open Proteomics Database. http://bioinformatics.icmb.utexas.edu/OPD/ (7 January 2008, date last accessed).
-
-
-
-
77
-
-
42049083408
-
-
Gene Expression Omnibus. http://www.ncbi.nlm.nih.gov/geo/ (7 January 2008, date last accessed).
-
Gene Expression Omnibus. http://www.ncbi.nlm.nih.gov/geo/ (7 January 2008, date last accessed).
-
-
-
-
78
-
-
42049107855
-
-
Proteome Harvest Spreadsheet. http://www.ebi.ac.uk/pride/ proteomeharvest/index.html (7 January 2008, date last accessed).
-
Proteome Harvest Spreadsheet. http://www.ebi.ac.uk/pride/ proteomeharvest/index.html (7 January 2008, date last accessed).
-
-
-
-
79
-
-
23944492134
-
Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database
-
Omenn GS, States DJ, Adamski M, et al. Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005;5:3226-45.
-
(2005)
Proteomics
, vol.5
, pp. 3226-3245
-
-
Omenn, G.S.1
States, D.J.2
Adamski, M.3
-
80
-
-
35648980489
-
Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics
-
Prakash A, Piening B, Whiteaker J, et al. Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics. Mol Cell Proteomics 2007;6:1741-8.
-
(2007)
Mol Cell Proteomics
, vol.6
, pp. 1741-1748
-
-
Prakash, A.1
Piening, B.2
Whiteaker, J.3
-
81
-
-
35848929694
-
Analysis and validation of proteomic data generated by tandem mass spectrometry
-
Nesvizhskii AI, Vitek O, Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 2007;4:787-97.
-
(2007)
Nat Methods
, vol.4
, pp. 787-797
-
-
Nesvizhskii, A.I.1
Vitek, O.2
Aebersold, R.3
-
82
-
-
42049099761
-
-
PEDRo Data Collator. http://pedrodownload.man.ac.uk/ (7 January 2008, date last accessed).
-
PEDRo Data Collator. http://pedrodownload.man.ac.uk/ (7 January 2008, date last accessed).
-
-
-
-
84
-
-
42049104427
-
-
Qurator. http://www.qurator.org/ (7 January 2008, date last accessed).
-
Qurator. http://www.qurator.org/ (7 January 2008, date last accessed).
-
-
-
-
85
-
-
42049088361
-
-
Taverna. http://taverna.sourceforge.net/ (7 January 2008, date last accessed).
-
Taverna. http://taverna.sourceforge.net/ (7 January 2008, date last accessed).
-
-
-
-
86
-
-
40249104592
-
Quality views: Capturing and exploiting the user perspective on data quality
-
Seoul, Korea
-
Missier P, Embury S, Greenwood M, et al. Quality views: Capturing and exploiting the user perspective on data quality. Proceedings of the 32nd International Conference on Very Large Data Bases (VLDB 2006), Seoul, Korea, 2006, 977-88.
-
(2006)
Proceedings of the 32nd International Conference on Very Large Data Bases (VLDB 2006)
, pp. 977-988
-
-
Missier, P.1
Embury, S.2
Greenwood, M.3
|