-
1
-
-
0037435030
-
Mass spectrometry-based proteomics
-
Aebersold, R. and Mann, M. (2003) Mass spectrometry-based proteomics. Nature, 422, 198-207.
-
(2003)
Nature
, vol.422
, pp. 198-207
-
-
Aebersold, R.1
Mann, M.2
-
2
-
-
77149158441
-
Unrestricted identification of modified proteins using MS/MS
-
Ahrne, E. et al. (2010) Unrestricted identification of modified proteins using MS/MS. Proteomics, 10, 671-686.
-
(2010)
Proteomics
, vol.10
, pp. 671-686
-
-
Ahrne, E.1
-
3
-
-
77951870981
-
A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry
-
Baliban, R.C. et al. (2010) A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry. Mol Cell Proteom., 9, 764-779.
-
(2010)
Mol Cell Proteom.
, vol.9
, pp. 764-779
-
-
Baliban, R.C.1
-
4
-
-
79957745193
-
Recent developments in quantitative proteomics
-
Becker, C.H. and Bern, M. (2011) Recent developments in quantitative proteomics. Mutation Res., 722, 171-182.
-
(2011)
Mutation Res.
, vol.722
, pp. 171-182
-
-
Becker, C.H.1
Bern, M.2
-
5
-
-
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. Royal Stat. Soc. Series B (Methodological), 57, 289-300.
-
(1995)
J. Royal Stat. Soc. Series B (Methodological)
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
6
-
-
53049109206
-
Conjugation of complex polyubiquitin chains to WRNIP1
-
Bish, R.A. et al. (2008) Conjugation of complex polyubiquitin chains to WRNIP1. J. Proteome Res., 7, 3481-3489.
-
(2008)
J. Proteome Res.
, vol.7
, pp. 3481-3489
-
-
Bish, R.A.1
-
7
-
-
38649110750
-
X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers
-
Bjornson, R.D. et al. (2008) X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers. J. Proteome Res., 7, 293-299.
-
(2008)
J. Proteome Res.
, vol.7
, pp. 293-299
-
-
Bjornson, R.D.1
-
8
-
-
58849092421
-
PTMap-A sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites
-
Chen, Y. et al. (2009) PTMap-a sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites. Proc. Natl Acad. Sci. USA, 106, 761-766.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 761-766
-
-
Chen, Y.1
-
10
-
-
79952613335
-
Computational refinement of post-translational modifications predicted from tandem mass spectrometry
-
Chung, C. et al. (2011) Computational refinement of post-translational modifications predicted from tandem mass spectrometry. Bioinformatics (Oxford, England), 27, 797-806.
-
(2011)
Bioinformatics (Oxford, England)
, vol.27
, pp. 797-806
-
-
Chung, C.1
-
11
-
-
0141955057
-
A method for reducing the time required to match protein sequences with tandem mass spectra
-
Craig, R. and Beavis, R.C. (2003) A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun. Mass Spectrom., 17, 2310-2316.
-
(2003)
Rapid Commun. Mass Spectrom.
, vol.17
, pp. 2310-2316
-
-
Craig, R.1
Beavis, R.C.2
-
12
-
-
3142702204
-
TANDEM: Matching proteins with tandem mass spectra
-
Craig, R. and Beavis, R.C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics (Oxford, England), 20, 1466-1467.
-
(2004)
Bioinformatics (Oxford, England)
, vol.20
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
13
-
-
11144320641
-
Open source system for analyzing, validating, and storing protein identification data
-
Craig, R. et al. (2004) Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res., 3, 1234-1242.
-
(2004)
J. Proteome Res.
, vol.3
, pp. 1234-1242
-
-
Craig, R.1
-
14
-
-
0036807449
-
Error tolerant searching of uninterpreted tandem mass spectrometry data
-
Creasy, D.M. and Cottrell, J.S. (2002) Error tolerant searching of uninterpreted tandem mass spectrometry data. Proteomics, 2, 1426-1434.
-
(2002)
Proteomics
, vol.2
, pp. 1426-1434
-
-
Creasy, D.M.1
Cottrell, J.S.2
-
15
-
-
41349096900
-
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
-
Deutsch, E.W. et al. (2008) Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol. Genom., 33, 18-25.
-
(2008)
Physiol. Genom.
, vol.33
, pp. 18-25
-
-
Deutsch, E.W.1
-
16
-
-
33847630405
-
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
-
Elias, J.E. and Gygi, S.P. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods, 4, 207-214.
-
(2007)
Nat. Methods
, vol.4
, pp. 207-214
-
-
Elias, J.E.1
Gygi, S.P.2
-
17
-
-
34247209215
-
Validated MALDI-TOF/TOF mass spectra for protein standards
-
Falkner, J.A. et al. (2007) Validated MALDI-TOF/TOF mass spectra for protein standards. J. Am. Soc. Mass Spectrom., 18, 850-855.
-
(2007)
J. Am. Soc. Mass Spectrom.
, vol.18
, pp. 850-855
-
-
Falkner, J.A.1
-
18
-
-
79955762105
-
DeltAMT: A statistical algorithm for fast detection of protein modifications from LC-MS/MS data
-
Fu, Y. et al. (2011) DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS/MS data. Mol. Cell Proteom., 10, M110 000455.
-
(2011)
Mol. Cell Proteom.
, vol.10
-
-
Fu, Y.1
-
19
-
-
0037250368
-
The RESID database of protein modifications: 2003 developments
-
Garavelli, J.S. (2003) The RESID database of protein modifications: 2003 developments. Nucleic Acids Res., 31, 499-501.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 499-501
-
-
Garavelli, J.S.1
-
20
-
-
7044246160
-
Open mass spectrometry search algorithm
-
Geer, L.Y. et al. (2004) Open mass spectrometry search algorithm. J. Proteome Res., 3, 958-964.
-
(2004)
J. Proteome Res.
, vol.3
, pp. 958-964
-
-
Geer, L.Y.1
-
21
-
-
58549085778
-
An integrated workflow for charting the human interaction proteome: Insights into the PP2A system
-
Glatter, T. et al. (2009) An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol. Syst. Biol., 5, 237.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 237
-
-
Glatter, T.1
-
23
-
-
17444383114
-
P-Mod: An algorithm and software to map modifications to peptide sequences using tandem MS data
-
Hansen, B.T. et al. (2005) P-Mod: an algorithm and software to map modifications to peptide sequences using tandem MS data. J. Proteome Res., 4, 358-368.
-
(2005)
J. Proteome Res.
, vol.4
, pp. 358-368
-
-
Hansen, B.T.1
-
24
-
-
84899829959
-
A formal basis for the heuristic determination of minimum cost paths
-
Hart, P.E., Nilsson, N.J. and Raphael, B. (1968) A formal basis for the heuristic determination of minimum cost paths. Systems Science and Cybernetics, 4, 100-107.
-
(1968)
Systems Science and Cybernetics
, vol.4
, pp. 100-107
-
-
Hart, P.E.1
Nilsson, N.J.2
Raphael, B.3
-
25
-
-
33847242627
-
Large-scale unrestricted identification of post-translation modifications using tandem mass spectrometry
-
Havilio, M. and Wool, A. (2007) Large-scale unrestricted identification of post-translation modifications using tandem mass spectrometry. Anal. Chem., 79, 1362-1368.
-
(2007)
Anal. Chem.
, vol.79
, pp. 1362-1368
-
-
Havilio, M.1
Wool, A.2
-
26
-
-
79952112647
-
Bioinformatics for LC-MS/MS-based proteomics
-
Jacob, R.J. (2010) Bioinformatics for LC-MS/MS-based proteomics. Methods Mol. Biol., 658, 61-91.
-
(2010)
Methods Mol. Biol.
, vol.658
, pp. 61-91
-
-
Jacob, R.J.1
-
27
-
-
84878045698
-
False discovery rates in spectral identification
-
Jeong, K. et al. (2012) False discovery rates in spectral identification. BMC Bioinform., 13 (Suppl 16), S2.
-
(2012)
BMC Bioinform.
, vol.13
, Issue.SUPPL. 16
-
-
Jeong, K.1
-
28
-
-
13844271209
-
Informatics for protein identification by mass spectrom-etry
-
Johnson, R.S. et al. (2005) Informatics for protein identification by mass spectrom-etry. Methods, 35, 223-236.
-
(2005)
Methods
, vol.35
, pp. 223-236
-
-
Johnson, R.S.1
-
29
-
-
38649083118
-
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
-
Kall, L. et al. (2007) Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J. Proteome Res., 7, 29-34.
-
(2007)
J. Proteome Res.
, vol.7
, pp. 29-34
-
-
Kall, L.1
-
30
-
-
3042818018
-
The International Protein Index: An integrated database for proteomics experiments
-
Kersey, P.J. et al. (2004) The International Protein Index: an integrated database for proteomics experiments. Proteomics, 4, 1985-1988.
-
(2004)
Proteomics
, vol.4
, pp. 1985-1988
-
-
Kersey, P.J.1
-
32
-
-
84861133742
-
Database searching in mass spectrometry based proteomics
-
Kertesz-Farkas, A. et al. (2012) Database searching in mass spectrometry based proteomics. Curr. Bioinform., 7, 221-230.
-
(2012)
Curr. Bioinform.
, vol.7
, pp. 221-230
-
-
Kertesz-Farkas, A.1
-
33
-
-
70450059712
-
PTMSearchPlus: Software tool for automated protein identification and post-translational modification characterization by integrating accurate intact protein mass and bottom-up mass spectrometric data searches
-
Kertesz, V. et al. (2009) PTMSearchPlus: software tool for automated protein identification and post-translational modification characterization by integrating accurate intact protein mass and bottom-up mass spectrometric data searches. Anal. Chem., 81, 8387-8395.
-
(2009)
Anal. Chem.
, vol.81
, pp. 8387-8395
-
-
Kertesz, V.1
-
34
-
-
33747837768
-
MODi: A powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra
-
Kim, S. et al. (2006) MODi: a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra. Nucleic Acids Res., 34, W258-W263.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Kim, S.1
-
35
-
-
54349102503
-
Sequential interval motif search: Unrestricted database surveys of global MS/MS data sets for detection of putative post-translational modifications
-
Liu, J. et al. (2008) Sequential interval motif search: unrestricted database surveys of global MS/MS data sets for detection of putative post-translational modifications. Anal. Chem., 80, 7846-7854.
-
(2008)
Anal. Chem.
, vol.80
, pp. 7846-7854
-
-
Liu, J.1
-
36
-
-
13444304209
-
Computational analysis of shotgun proteomics data
-
MacCoss, M.J. (2005) Computational analysis of shotgun proteomics data. Curr. Opin. Chem. Biol., 9, 88-94.
-
(2005)
Curr. Opin. Chem. Biol.
, vol.9
, pp. 88-94
-
-
Maccoss, M.J.1
-
37
-
-
18444391517
-
Shotgun identification of protein modifications from protein complexes and lens tissue
-
MacCoss, M.J. et al. (2002) Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl Acad. Sci. USA, 99, 7900-7905.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 7900-7905
-
-
Maccoss, M.J.1
-
38
-
-
33750979860
-
General framework for developing and evaluating database scoring algorithms using the TANDEM search engine
-
MacLean, B., Eng, J.K., Beavis, R.C. and McIntosh, M. (2006) General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics, 22, 2830-2832.
-
(2006)
Bioinformatics
, vol.22
, pp. 2830-2832
-
-
Maclean, B.1
Eng, J.K.2
Beavis, R.C.3
McIntosh, M.4
-
39
-
-
4544280727
-
MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications
-
McDonald, W.H. et al. (2004) MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun. Mass Spectrom., 18, 2162-2168.
-
(2004)
Rapid Commun. Mass Spectrom.
, vol.18
, pp. 2162-2168
-
-
McDonald, W.H.1
-
40
-
-
77952014893
-
Peptidomics coming of age: A review of contributions from a bioinformatics angle
-
Menschaert, G. et al. (2010) Peptidomics coming of age: a review of contributions from a bioinformatics angle. J. Proteome Res., 9, 2051-2061.
-
(2010)
J. Proteome Res.
, vol.9
, pp. 2051-2061
-
-
Menschaert, G.1
-
41
-
-
0036209134
-
Qscore: An algorithm for evaluating SEQUEST database search results
-
Moore, R.E. et al. (2002) Qscore: an algorithm for evaluating SEQUEST database search results. J. Am. Soc. Mass Spectrom., 13, 378-386.
-
(2002)
J. Am. Soc. Mass Spectrom.
, vol.13
, pp. 378-386
-
-
Moore, R.E.1
-
42
-
-
77957221582
-
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
-
Nesvizhskii, A.I. (2010) A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J. Proteom., 73, 2092-2123.
-
(2010)
J. Proteom.
, vol.73
, pp. 2092-2123
-
-
Nesvizhskii, A.I.1
-
43
-
-
1042266254
-
Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS
-
Nesvizhskii, A.I. and Aebersold, R. (2004) Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov. Today, 9, 173-181.
-
(2004)
Drug Discov. Today
, vol.9
, pp. 173-181
-
-
Nesvizhskii, A.I.1
Aebersold, R.2
-
44
-
-
78650173423
-
Computational mass spectrometry for metabo-lomics: Identification of metabolites and small molecules
-
Neumann, S. and Bocker, S. (2010) Computational mass spectrometry for metabo-lomics: identification of metabolites and small molecules. Anal. Bioanalyt. Chem., 398, 2779-2788.
-
(2010)
Anal. Bioanalyt. Chem.
, vol.398
, pp. 2779-2788
-
-
Neumann, S.1
Bocker, S.2
-
45
-
-
84857476737
-
Computational and statistical analysis of protein mass spectrometry data
-
Noble, W.S. and MacCoss, M.J. (2012) Computational and statistical analysis of protein mass spectrometry data. PLoS Comput Biol., 8, e1002296.
-
(2012)
PLoS Comput Biol.
, vol.8
-
-
Noble, W.S.1
Maccoss, M.J.2
-
46
-
-
1942423061
-
High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results
-
Searle, B.C. et al. (2004) High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results. Anal. Chem., 76, 2220-2230.
-
(2004)
Anal. Chem.
, vol.76
, pp. 2220-2230
-
-
Searle, B.C.1
-
47
-
-
43149103140
-
ROC analysis: Applications to the classification of biological sequences and 3D structures
-
Sonego, P. et al. (2008) ROC analysis: applications to the classification of biological sequences and 3D structures. Brief. Bioinform., 9, 198-209.
-
(2008)
Brief. Bioinform.
, vol.9
, pp. 198-209
-
-
Sonego, P.1
-
48
-
-
38649111957
-
Accurate annotation of peptide modifications through unrestrictive database search
-
Tanner, S. et al. (2008) Accurate annotation of peptide modifications through unrestrictive database search. J. Proteome Res., 7, 170-181.
-
(2008)
J. Proteome Res.
, vol.7
, pp. 170-181
-
-
Tanner, S.1
-
49
-
-
77949752005
-
Data maximization by multipass analysis of protein mass spectra
-
Tharakan, R. et al. (2010) Data maximization by multipass analysis of protein mass spectra. Proteomics, 10, 1160-1171.
-
(2010)
Proteomics
, vol.10
, pp. 1160-1171
-
-
Tharakan, R.1
-
50
-
-
33745502894
-
Identification of post-translational modifications via blind search of mass-spectra. In: Proceedings/
-
CSB, San Francisco, CA, USA.
-
Tsur, D. et al. (2005) Identification of post-translational modifications via blind search of mass-spectra. In: Proceedings/IEEE Computational Systems Bioinformatics Conference, CSB, San Francisco, CA, USA. pp. 157-166.
-
(2005)
IEEE Computational Systems Bioinformatics Conference
, pp. 157-166
-
-
Tsur, D.1
-
51
-
-
36349024645
-
Current trends in computational inference from mass spectrometry-based proteomics
-
Webb-Robertson, B.J. and Cannon, W.R. (2007) Current trends in computational inference from mass spectrometry-based proteomics. Brief. Bioinform., 8, 304-317.
-
(2007)
Brief. Bioinform.
, vol.8
, pp. 304-317
-
-
Webb-Robertson, B.J.1
Cannon, W.R.2
-
52
-
-
0029644596
-
Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database
-
Yates, J.R. 3rd et al. (1995) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem., 67, 1426-1436.
-
(1995)
Anal. Chem.
, vol.67
, pp. 1426-1436
-
-
Yates III, J.R.1
-
53
-
-
77954191980
-
Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate
-
Ye, D. et al. (2010) Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate. Bioinformatics (Oxford, England), 26, i399-i406.
-
(2010)
Bioinformatics (Oxford, England)
, vol.26
-
-
Ye, D.1
|