-
1
-
-
13444283630
-
Interaction network containing conserved and essential protein complexes in Escherichia coli
-
DOI 10.1038/nature03239
-
Butland, G. Interaction network containing conserved and essential protein complexes in Escherichia coli Nature 2005, 433, 531-537 (Pubitemid 40204311)
-
(2005)
Nature
, vol.433
, Issue.7025
, pp. 531-537
-
-
Butland, G.1
Peregrin-Alvarez, J.M.2
Li, J.3
Yang, W.4
Yang, X.5
Canadien, V.6
Starostine, A.7
Richards, D.8
Beattie, B.9
Krogan, N.10
Davey, M.11
Parkinson, J.12
Greenblatt, J.13
Emili, A.14
-
2
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
Gavin, A. C. Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002, 415, 141-147
-
(2002)
Nature
, vol.415
, pp. 141-147
-
-
Gavin, A.C.1
-
3
-
-
0037050004
-
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
-
DOI 10.1038/415180a
-
Ho, Y. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 2002, 415, 180-183 (Pubitemid 34059520)
-
(2002)
Nature
, vol.415
, Issue.6868
, pp. 180-183
-
-
Ho, Y.1
Gruhler, A.2
Heilbut, A.3
Bader, G.D.4
Moore, L.5
Adams, S.-L.6
Millar, A.7
Taylor, P.8
Bennett, K.9
Boutilier, K.10
Yang, L.11
Wolting, C.12
Donaldson, I.13
Schandorff, S.14
Shewnarane, J.15
Vo, M.16
Taggart, J.17
Goudreault, M.18
Muskat, B.19
Alfarano, C.20
Dewar, D.21
Lin, Z.22
Michalickova, K.23
Willems, A.R.24
Sassi, H.25
Nielsen, P.A.26
Rasmussen, K.J.27
Andersen, J.R.28
Johansen, L.E.29
Hansen, L.H.30
Jespersen, H.31
Podtelejnikov, A.32
Nielsen, E.33
Crawford, J.34
Poulsen, V.35
Sorensen, B.D.36
Matthiesen, J.37
Hendrickson, R.C.38
Gleeson, F.39
Pawson, T.40
Moran, M.F.41
Durocher, D.42
Mann, M.43
Hogue, C.W.V.44
Figeys, D.45
Tyers, M.46
more..
-
4
-
-
0033593013
-
Activity-based protein profiling: The serine hydrolases
-
DOI 10.1073/pnas.96.26.14694
-
Liu, Y.; Patricelli, M. P.; Cravatt, B. F. Activity-based protein profiling: the serine hydrolases Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14694-14699 (Pubitemid 30019702)
-
(1999)
Proceedings of the National Academy of Sciences of the United States of America
, vol.96
, Issue.26
, pp. 14694-14699
-
-
Liu, Y.1
Patricelli, M.P.2
Cravatt, B.F.3
-
5
-
-
78650611536
-
Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome
-
Burnum, K. E.; Callister, S. J.; Nicora, C. D.; Purvine, S. O.; Hugenholtz, P.; Warnecke, F.; Scheffrahn, R. H.; Smith, R. D.; Lipton, M. S. Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome ISME J. 2011, 5 (1) 161-4
-
(2011)
ISME J.
, vol.5
, Issue.1
, pp. 161-4
-
-
Burnum, K.E.1
Callister, S.J.2
Nicora, C.D.3
Purvine, S.O.4
Hugenholtz, P.5
Warnecke, F.6
Scheffrahn, R.H.7
Smith, R.D.8
Lipton, M.S.9
-
6
-
-
34047169728
-
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
-
DOI 10.1038/nature05624, PII NATURE05624
-
Lo, I. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria Nature 2007, 446, 537-541 (Pubitemid 46514723)
-
(2007)
Nature
, vol.446
, Issue.7135
, pp. 537-541
-
-
Lo, I.1
Denef, V.J.2
VerBerkmoes, N.C.3
Shah, M.B.4
Goltsman, D.5
DiBartolo, G.6
Tyson, G.W.7
Allen, E.E.8
Ram, R.J.9
Detter, J.C.10
Richardson, P.11
Thelen, M.P.12
Hettich, R.L.13
Banfield, J.F.14
-
7
-
-
46349085804
-
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
-
DOI 10.1093/bioinformatics/btn218
-
Webb-Robertson, B. J.; Cannon, W. R. A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics Bioinformatics (Oxford, England) 2008, 24 (13) 1503-9 (Pubitemid 351916567)
-
(2008)
Bioinformatics
, vol.24
, Issue.13
, pp. 1503-1509
-
-
Webb-Robertson, B.-J.M.1
Cannon, W.R.2
Oehmen, C.S.3
Shah, A.R.4
Gurumoorthi, V.5
Lipton, M.S.6
Waters, K.M.7
-
8
-
-
21744435622
-
Scoring proteomes with proteotypic peptide probes
-
DOI 10.1038/nrm1683
-
Kuster, B.; Schirle, M.; Mallick, P.; Aebersold, R. Scoring proteomes with proteotypic peptide probes Nat. Rev. Mol. Cell. Biol. 2005, 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
-
9
-
-
33846133955
-
Computational prediction of proteotypic peptides for quantitative proteomics
-
DOI 10.1038/nbt1275, PII NBT1275
-
Mallick, P. Computational prediction of proteotypic peptides for quantitative proteomics Nat. Biotechnol. 2007, 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
-
10
-
-
33747885134
-
A computational approach toward label-free protein quantification using predicted peptide detectability
-
Tang, H. A computational approach toward label-free protein quantification using predicted peptide detectability Bioinformatics 2006, 22, e481-488
-
(2006)
Bioinformatics
, vol.22
, pp. 481-488
-
-
Tang, H.1
-
11
-
-
34447313945
-
How do shotgun proteomics algorithms identify proteins?
-
DOI 10.1038/nbt0707-755, PII NBT0707755
-
Marcotte, E. M. How do shotgun proteomics algorithms identify proteins? Nat. Biotechnol. 2007, 25, 755-757 (Pubitemid 47053867)
-
(2007)
Nature Biotechnology
, vol.25
, Issue.7
, pp. 755-757
-
-
Marcotte, E.M.1
-
12
-
-
36349024645
-
Current trends in computational inference from mass spectrometry-based proteomics
-
DOI 10.1093/bib/bbm023, Special Issue: Current Progress in Bioinformatics: 2007
-
Webb-Robertson, B. J.; Cannon, W. R. Current trends in computational inference from mass spectrometry-based proteomics Brief. Bioinform. 2007, 8 (5) 304-17 (Pubitemid 350142620)
-
(2007)
Briefings in Bioinformatics
, vol.8
, Issue.5
, pp. 304-317
-
-
Webb-Robertson, B.-J.M.1
Cannon, W.R.2
-
13
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng, K.; McCormack, A. L.; Yates, J. R., III 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, K.1
McCormack, A.L.2
Yates III, J.R.3
-
14
-
-
0032750293
-
De novo peptide sequencing via tandem mass spectrometry
-
Dancik, V.; Addona, T. A.; Clauser, K. R.; Vath, J. E.; Pevzner, P. A. De novo peptide sequencing via tandem mass spectrometry J. Comput. Biol. 1999, 6, 327-342
-
(1999)
J. Comput. Biol.
, vol.6
, pp. 327-342
-
-
Dancik, V.1
Addona, T.A.2
Clauser, K.R.3
Vath, J.E.4
Pevzner, P.A.5
-
15
-
-
0037353846
-
Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides
-
DOI 10.1021/ac026122m
-
Tabb, D. L. Statistical characterization of ion trap mass spectra from doubly charged tryptic peptides Anal. Chem. 2003, 75, 1155-1163 (Pubitemid 36402645)
-
(2003)
Analytical Chemistry
, vol.75
, Issue.5
, pp. 1155-1163
-
-
Tabb, D.L.1
Smith, L.L.2
Breci, L.A.3
Wysocki, V.H.4
Lin, D.5
Yates III, J.R.6
-
16
-
-
63049121561
-
A simple workflow to increase MS2 identification rate by subsequent spectral library search
-
Ahrne, E.; Masselot, A.; Binz, P. A.; Muller, M.; Lisacek, F. A simple workflow to increase MS2 identification rate by subsequent spectral library search Proteomics 2009, 9, 1731-1736
-
(2009)
Proteomics
, vol.9
, pp. 1731-1736
-
-
Ahrne, E.1
Masselot, A.2
Binz, P.A.3
Muller, M.4
Lisacek, F.5
-
17
-
-
1842580753
-
Improving large-scale proteomics by clustering of mass spectrometry data
-
DOI 10.1002/pmic.200300652
-
Beer, I.; Barnea, E.; Ziv, T.; Admon, A. Improving large-scale proteomics by clustering of mass spectrometry data Proteomics 2004, 4, 950-960 (Pubitemid 38445955)
-
(2004)
Proteomics
, vol.4
, Issue.4
, pp. 950-960
-
-
Beer, I.1
Barnea, E.2
Ziv, T.3
Admon, A.4
-
18
-
-
33747170146
-
Using annotated peptide mass spectrum libraries for protein identification
-
DOI 10.1021/pr0602085
-
Craig, R.; Cortens, J. C.; Fenyo, D.; Beavis, R. C. Using annotated peptide mass spectrum libraries for protein identification J. Proteome Res. 2006, 5, 1843-1849 (Pubitemid 44232697)
-
(2006)
Journal of Proteome Research
, vol.5
, Issue.8
, pp. 1843-1849
-
-
Craig, R.1
Cortens, J.C.2
Fenyo, D.3
Beavis, R.C.4
-
19
-
-
0032159387
-
Method to compare collision-induced dissociation spectra of peptides: Potential for library searching and subtractive analysis
-
Yates, J. R., 3rd; Morgan, S. F.; Gatlin, C. L.; Griffin, P. R.; Eng, J. K. Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis Anal. Chem. 1998, 70, 3557-3565
-
(1998)
Anal. Chem.
, vol.70
, pp. 3557-3565
-
-
Yates III, Y.J.1
Morgan, S.F.2
Gatlin, C.L.3
Griffin, P.R.4
Eng, J.K.5
-
20
-
-
3042735333
-
High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics
-
DOI 10.1002/pmic.200300708
-
Colinge, J. High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics Proteomics 2004, 4, 1977-1984 (Pubitemid 38880362)
-
(2004)
Proteomics
, vol.4
, Issue.7
, pp. 1977-1984
-
-
Colinge, J.1
Masselot, A.2
Cusin, I.3
Mahe, E.4
Niknejad, A.5
Argoud-Puy, G.6
Reffas, S.7
Bederr, N.8
Gleizes, A.9
Pierre-Antoine, R.10
Bougueleret, L.11
-
21
-
-
34548133443
-
Development and validation of a spectral library searching method for human peptide identification from tandem mass spectrometry
-
Lam, H. Development and validation of a spectral library searching method for human peptide identification from tandem mass spectrometry Mol. Cell. Proteomics 2006, 5, S361-S361
-
(2006)
Mol. Cell. Proteomics
, vol.5
-
-
Lam, H.1
-
22
-
-
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.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal. Chem. 2002, 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
-
-
26844570632
-
Comparison of probability and likelihood models for peptide identification from tandem mass spectrometry data
-
DOI 10.1021/pr050147v
-
Cannon, W. R. A Comparison of Probability and Likelihood Models for Peptide Identification from Tandem Mass Spectrometry Data J. Proteome Res. 2005, 4, 1687-1698 (Pubitemid 41464796)
-
(2005)
Journal of Proteome Research
, vol.4
, Issue.5
, pp. 1687-1698
-
-
Cannon, W.R.1
Jarman, K.H.2
Webb-Robertson, B.-J.M.3
Baxter, D.J.4
Oehmen, C.S.5
Jarman, K.D.6
Heredia-Langner, A.7
Auberry, K.J.8
Anderson, G.A.9
-
25
-
-
77950279914
-
Physicochemical/Thermodynamic Framework for the Interpretation of Peptide Tandem Mass Spectra
-
Cannon, W. R.; Rawlins, M. M. Physicochemical/Thermodynamic Framework for the Interpretation of Peptide Tandem Mass Spectra J. Phys. Chem. C 2010, 114, 5360-5366
-
(2010)
J. Phys. Chem. C
, vol.114
, pp. 5360-5366
-
-
Cannon, W.R.1
Rawlins, M.M.2
-
26
-
-
33750970838
-
Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes
-
DOI 10.1016/j.mimet.2006.04.021, PII S0167701206001242
-
Callister, S. J. Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes J. Microbiol. Methods 2006, 67, 424-436 (Pubitemid 44740199)
-
(2006)
Journal of Microbiological Methods
, vol.67
, Issue.3
, pp. 424-436
-
-
Callister, S.J.1
Nicora, C.D.2
Zeng, X.3
Roh, J.H.4
Dominguez, M.A.5
Tavano, C.L.6
Monroe, M.E.7
Kaplan, S.8
Donohue, T.J.9
Smith, R.D.10
Lipton, M.S.11
-
27
-
-
77952564899
-
Loss of the response regulator CtrA causes pleiotropic effects on gene expression but does not affect growth phase regulation in Rhodobacter capsulatus
-
Mercer, R. G. Loss of the response regulator CtrA causes pleiotropic effects on gene expression but does not affect growth phase regulation in Rhodobacter capsulatus J. Bacteriol. 2010, 192, 2701-2710
-
(2010)
J. Bacteriol.
, vol.192
, pp. 2701-2710
-
-
Mercer, R.G.1
-
28
-
-
41349120246
-
DeconMSn: A software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra
-
DOI 10.1093/bioinformatics/btn063
-
Mayampurath, A. M. DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra Bioinformatics 2008, 24, 1021-1023 (Pubitemid 351448041)
-
(2008)
Bioinformatics
, vol.24
, Issue.7
, pp. 1021-1023
-
-
Mayampurath, A.M.1
Jaitly, N.2
Purvine, S.O.3
Monroe, M.E.4
Auberry, K.J.5
Adkins, J.N.6
Smith, R.D.7
-
29
-
-
7044241336
-
Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis
-
DOI 10.1089/omi.2004.8.239
-
Romine, M. F. Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis Omics 2004, 8, 239-254 (Pubitemid 39425674)
-
(2004)
OMICS A Journal of Integrative Biology
, vol.8
, Issue.3
, pp. 239-254
-
-
Romine, M.F.1
Elias, D.A.2
Monroe, M.E.3
Auberry, K.4
Fang, R.5
Fredrickson, J.K.6
Anderson, G.A.7
Smith, R.D.8
Lipton, M.S.9
-
30
-
-
35748972060
-
Semi-supervised learning for peptide identification from shotgun proteomics datasets
-
DOI 10.1038/nmeth1113, PII NMETH1113
-
Kall, 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 (Pubitemid 350042380)
-
(2007)
Nature Methods
, vol.4
, Issue.11
, pp. 923-925
-
-
Kall, L.1
Canterbury, J.D.2
Weston, J.3
Noble, W.S.4
MacCoss, M.J.5
-
31
-
-
0001070119
-
Maximum-Likelihood-Estimation of the Parameters of the Generalized Extreme-Value Distribution
-
Hosking, J. R. M. Maximum-Likelihood-Estimation of the Parameters of the Generalized Extreme-Value Distribution Appl. Stat.-J. R. Soc. C 1985, 34, 301-310
-
(1985)
Appl. Stat.-J. R. Soc. C
, vol.34
, pp. 301-310
-
-
Hosking, J.R.M.1
-
32
-
-
63549095080
-
QVALITY: Non-parametric estimation of q-values and posterior error probabilities
-
Kall, L.; Storey, J. D.; Noble, W. S. QVALITY: non-parametric estimation of q-values and posterior error probabilities Bioinformatics (Oxford, England) 2009, 25, 964-966
-
(2009)
Bioinformatics (Oxford, England)
, vol.25
, pp. 964-966
-
-
Kall, L.1
Storey, J.D.2
Noble, W.S.3
-
34
-
-
70349213754
-
A bayesian approach to protein inference problem in shotgun proteomics
-
doi: 10.1089/cmb.2009.0018.
-
Li, Y. F. A bayesian approach to protein inference problem in shotgun proteomics. J. Comput. Biol. 16, 1183-1193, doi: 10.1089/cmb.2009.0018 (2009).
-
(2009)
J. Comput. Biol
, vol.16
, pp. 1183-1193
-
-
Li, Y.F.1
-
35
-
-
77957339566
-
Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data
-
Serang, O.; MacCoss, M. J.; Noble, W. S. Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data J. Proteome Res. 2010, 9, 5346-5357
-
(2010)
J. Proteome Res.
, vol.9
, pp. 5346-5357
-
-
Serang, O.1
MacCoss, M.J.2
Noble, W.S.3
-
36
-
-
0037317111
-
Intensity-based statistical scorer for tandem mass spectrometry
-
DOI 10.1021/ac0258913
-
Havilio, M.; Haddad, Y.; Smilansky, Z. Intensity-based statistical scorer for tandem mass spectrometry Anal. Chem. 2003, 75, 435-444 (Pubitemid 36176713)
-
(2003)
Analytical Chemistry
, vol.75
, Issue.3
, pp. 435-444
-
-
Havilio, M.1
Haddad, Y.2
Smilansky, Z.3
-
37
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
DOI 10.1093/nar/gki866
-
Overbeek, R. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes Nucleic Acids Res. 2005, 33, 5691-5702 (Pubitemid 41548835)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.17
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.-Y.5
Cohoon, M.6
De Crecy-Lagard, V.7
Diaz, N.8
Disz, T.9
Edwards, R.10
Fonstein, M.11
Frank, E.D.12
Gerdes, S.13
Glass, E.M.14
Goesmann, A.15
Hanson, A.16
Iwata-Reuyl, D.17
Jensen, R.18
Jamshidi, N.19
Krause, L.20
Kubal, M.21
Larsen, N.22
Linke, B.23
McHardy, A.C.24
Meyer, F.25
Neuweger, H.26
Olsen, G.27
Olson, R.28
Osterman, A.29
Portnoy, V.30
Pusch, G.D.31
Rodionov, D.A.32
Rul33
ckert, C.34
Steiner, J.35
Stevens, R.36
Thiele, I.37
Vassieva, O.38
Ye, Y.39
Zagnitko, O.40
Vonstein, V.41
more..
|