-
1
-
-
79551549643
-
Comprehensive proteomics
-
Beck, M., Claassen, M., and Aebersold, R. (2011) Comprehensive proteomics. Curr. Opin. Biotechnol. 22, 3-8
-
(2011)
Curr. Opin. Biotechnol.
, vol.22
, pp. 3-8
-
-
Beck, M.1
Claassen, M.2
Aebersold, R.3
-
2
-
-
0031568420
-
Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the lowfemtomole level
-
McCormack, A. L., Schieltz, D. M., Goode, B., Yang, S., Barnes, G., Drubin, D., and Yates, J. R., 3rd (1997) Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the lowfemtomole level. Anal. Chem. 69, 767-776
-
(1997)
Anal. Chem.
, vol.69
, pp. 767-776
-
-
McCormack, A.L.1
Schieltz, D.M.2
Goode, B.3
Yang, S.4
Barnes, G.5
Drubin, D.6
Yates III, J.R.7
-
3
-
-
41349096900
-
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
-
DOI 10.1152/physiolgenomics.00298.2007
-
Deutsch, E. W., Lam, H., and Aebersold, R. (2008) Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol. Genomics 33, 18-25 (Pubitemid 351451370)
-
(2008)
Physiological Genomics
, vol.33
, Issue.1
, pp. 18-25
-
-
Deutsch, E.W.1
Lam, H.2
Aebersold, R.3
-
4
-
-
40149085553
-
Thou shalt share your data
-
Nature Methods
-
Nature Methods (2008) Thou shalt share your data. Nat. Methods 5, 209
-
(2008)
Nat. Methods
, vol.5
, pp. 209
-
-
-
5
-
-
35349005184
-
Five years of progress in the Standardization of Proteomics Data 4(th) Annual Spring Workshop of the HUPO-Proteomics Standards Initiative, April 23-25, 2007, Ecole Nationale Superieure (ENS), Lyon, France
-
Orchard, S., Montechi-Palazzi, L., Deutsch, E. W., Binz, P. A., Jones, A. R., Paton, N., Pizarro, A., Creasy, D. M., Wojcik, J., and Hermjakob, H. (2007) Five years of progress in the Standardization of Proteomics Data 4(th) Annual Spring Workshop of the HUPO-Proteomics Standards Initiative, April 23-25, 2007, Ecole Nationale Superieure (ENS), Lyon, France. Proteomics 7, 3436-3440
-
(2007)
Proteomics
, vol.7
, pp. 3436-3440
-
-
Orchard, S.1
Montechi-Palazzi, L.2
Deutsch, E.W.3
Binz, P.A.4
Jones, A.R.5
Paton, N.6
Pizarro, A.7
Creasy, D.M.8
Wojcik, J.9
Hermjakob, H.10
-
6
-
-
77956125167
-
The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative
-
Gibson, F., Hoogland, C., Martinez-Bartolome, S., Medina-Aunon, J. A., Albar, J. P., Babnigg, G., Wipat, A., Hermjakob, H., Almeida, J. S., Stanislaus, R., Paton, N. W., and Jones, A. R. (2010) The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. Proteomics 10, 3073-3081
-
(2010)
Proteomics
, vol.10
, pp. 3073-3081
-
-
Gibson, F.1
Hoogland, C.2
Martinez-Bartolome, S.3
Medina-Aunon, J.A.4
Albar, J.P.5
Babnigg, G.6
Wipat, A.7
Hermjakob, H.8
Almeida, J.S.9
Stanislaus, R.10
Paton, N.W.11
Jones, A.R.12
-
7
-
-
60549084744
-
Managing the data explosion. A report on the HUPOPSI Workshop. August 2008, Amsterdam, the Netherlands
-
Orchard, S., Hoogland, C., Bairoch, A., Eisenacher, M., Kraus, H. J., and Binz, P. A. (2009) Managing the data explosion. A report on the HUPOPSI Workshop. August 2008, Amsterdam, The Netherlands. Proteomics 9, 499-501
-
(2009)
Proteomics
, vol.9
, pp. 499-501
-
-
Orchard, S.1
Hoogland, C.2
Bairoch, A.3
Eisenacher, M.4
Kraus, H.J.5
Binz, P.A.6
-
8
-
-
35148889036
-
The Functional Genomics Experiment model (FuGE): An extensible framework for standards in functional genomics
-
DOI 10.1038/nbt1347, PII NBT1347
-
Jones, A. R., Miller, M., Aebersold, R., Apweiler, R., Ball, C. A., Brazma, A., Degreef, J., Hardy, N., Hermjakob, H., Hubbard, S. J., Hussey, P., Igra, M., Jenkins, H., Julian, R. K., Jr., Laursen, K., Oliver, S. G., Paton, N. W., Sansone, S. A., Sarkans, U., Stoeckert, C. J., Jr., Taylor, C. F., Whetzel, P. L., White, J. A., Spellman, P., and Pizarro, A. (2007) The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat. Biotechnol. 25, 1127-1133 (Pubitemid 47538118)
-
(2007)
Nature Biotechnology
, vol.25
, Issue.10
, pp. 1127-1133
-
-
Jones, A.R.1
Miller, M.2
Aebersold, R.3
Apweiler, R.4
Ball, C.A.5
Brazma, A.6
DeGreef, J.7
Hardy, N.8
Hermjakob, H.9
Hubbard, S.J.10
Hussey, P.11
Igra, M.12
Jenkins, H.13
Julian Jr., R.K.14
Laursen, K.15
Oliver, S.G.16
Paton, N.W.17
Sansone, S.-A.18
Sarkans, U.19
Stoeckert Jr., C.J.20
Taylor, C.F.21
Whetzel, P.L.22
White, J.A.23
Spellman, P.24
Pizarro, A.25
more..
-
9
-
-
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
-
10
-
-
84859843750
-
TraML - A standard format for exchange of selected reaction monitoring transition lists
-
Deutsch, E. W., Chambers, M., Neumann, S., Levander, F., Binz, P. A., Shofstahl, J., Campbell, D. S., Mendoza, L., Ovelleiro, D., Helsens, K., Martens, L., Aebersold, R., Moritz, R. L., and Brusniak, M. Y. (2012) TraML - a standard format for exchange of selected reaction monitoring transition lists. Mol. Cell. Proteomics 11, R111.015040
-
(2012)
Mol. Cell. Proteomics
, vol.11
-
-
Deutsch, E.W.1
Chambers, M.2
Neumann, S.3
Levander, F.4
Binz, P.A.5
Shofstahl, J.6
Campbell, D.S.7
Mendoza, L.8
Ovelleiro, D.9
Helsens, K.10
Martens, L.11
Aebersold, R.12
Moritz, R.L.13
Brusniak, M.Y.14
-
11
-
-
84863624355
-
Automated selected reaction monitoring software for accurate label-free protein quantification
-
Teleman, J., Karlsson, C., Waldemarson, S., Hansson, K., James, P., Malmstrom, J., and Levander, F. (2012) Automated selected reaction monitoring software for accurate label-free protein quantification. J. Proteome Res. 11, 3766-3773
-
(2012)
J. Proteome Res.
, vol.11
, pp. 3766-3773
-
-
Teleman, J.1
Karlsson, C.2
Waldemarson, S.3
Hansson, K.4
James, P.5
Malmstrom, J.6
Levander, F.7
-
12
-
-
79952703214
-
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry
-
Brusniak, M. Y., Kwok, S. T., Christiansen, M., Campbell, D., Reiter, L., Picotti, P., Kusebauch, U., Ramos, H., Deutsch, E. W., Chen, J., Moritz, R. L., and Aebersold, R. (2011) ATAQS: a computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. BMC Bioinformatics 12, 78
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 78
-
-
Brusniak, M.Y.1
Kwok, S.T.2
Christiansen, M.3
Campbell, D.4
Reiter, L.5
Picotti, P.6
Kusebauch, U.7
Ramos, H.8
Deutsch, E.W.9
Chen, J.10
Moritz, R.L.11
Aebersold, R.12
-
13
-
-
80655129284
-
JTraML: An open source java API for TraML, the PSI standard for sharing SRM transitions
-
Helsens, K., Brusniak, M. Y., Deutsch, E., Moritz, R. L., and Martens, L. (2011) jTraML: an open source java API for TraML, the PSI standard for sharing SRM transitions. J. Proteome Res. 10, 5260-5263
-
(2011)
J. Proteome Res.
, vol.10
, pp. 5260-5263
-
-
Helsens, K.1
Brusniak, M.Y.2
Deutsch, E.3
Moritz, R.L.4
Martens, L.5
-
14
-
-
42249108173
-
OpenMS - An open-source software framework for mass spectrometry
-
Sturm, M., Bertsch, A., Gropl, C., Hildebrandt, A., Hussong, R., Lange, E., Pfeifer, N., Schulz-Trieglaff, O., Zerck, A., Reinert, K., and Kohlbacher, O. (2008) OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics 9, 163
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 163
-
-
Sturm, M.1
Bertsch, A.2
Gropl, C.3
Hildebrandt, A.4
Hussong, R.5
Lange, E.6
Pfeifer, N.7
Schulz-Trieglaff, O.8
Zerck, A.9
Reinert, K.10
Kohlbacher, O.11
-
15
-
-
67049100049
-
The proteios software environment: An extensible multiuser platform for management and analysis of proteomics data
-
Hakkinen, J., Vincic, G., Mansson, O., Warell, K., and Levander, F. (2009) The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data. J. Proteome Res. 8, 3037-3043
-
(2009)
J. Proteome Res.
, vol.8
, pp. 3037-3043
-
-
Hakkinen, J.1
Vincic, G.2
Mansson, O.3
Warell, K.4
Levander, F.5
-
16
-
-
77951965920
-
Skyline: An open source document editor for creating and analyzing targeted proteomics experiments
-
MacLean, B., Tomazela, D. M., Shulman, N., Chambers, M., Finney, G. L., Frewen, B., Kern, R., Tabb, D. L., Liebler, D. C., and MacCoss, M. J. (2010) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966-968
-
(2010)
Bioinformatics
, vol.26
, pp. 966-968
-
-
MacLean, B.1
Tomazela, D.M.2
Shulman, N.3
Chambers, M.4
Finney, G.L.5
Frewen, B.6
Kern, R.7
Tabb, D.L.8
Liebler, D.C.9
MacCoss, M.J.10
-
17
-
-
3543030998
-
Should software hold data hostage?
-
DOI 10.1038/nbt0804-1037
-
Wiley, H. S., and Michaels, G. S. (2004) Should software hold data hostage? Nat. Biotechnol. 22, 1037-1038 (Pubitemid 39014485)
-
(2004)
Nature Biotechnology
, vol.22
, Issue.8
, pp. 1037-1038
-
-
Wiley, H.S.1
Michaels, G.S.2
-
18
-
-
23944440436
-
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories
-
DOI 10.1002/pmic.200401302
-
Martens, L., Nesvizhskii, A. I., Hermjakob, H., Adamski, M., Omenn, G. S., Vandekerckhove, J., and Gevaert, K. (2005) Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories. Proteomics 5, 3501-3505 (Pubitemid 41192055)
-
(2005)
Proteomics
, vol.5
, Issue.13
, pp. 3501-3505
-
-
Martens, L.1
Nesvizhskii, A.I.2
Hermjakob, H.3
Adamski, M.4
Omenn, G.S.5
Vandekerckhove, J.6
Gevaert, K.7
-
19
-
-
8344284323
-
A common open representation of mass spectrometry data and its application to proteomics research
-
DOI 10.1038/nbt1031
-
Pedrioli, P. G., Eng, J. K., Hubley, R., Vogelzang, M., Deutsch, E. W., Raught, B., Pratt, B., Nilsson, E., Angeletti, R. H., Apweiler, R., Cheung, K., Costello, C. E., Hermjakob, H., Huang, S., Julian, R. K., Kapp, E., McComb, M. E., Oliver, S. G., Omenn, G., Paton, N. W., Simpson, R., Smith, R., Taylor, C. F., Zhu, W., and Aebersold, R. (2004) A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 22, 1459-1466 (Pubitemid 39482868)
-
(2004)
Nature Biotechnology
, vol.22
, Issue.11
, pp. 1459-1466
-
-
Pedrioli, P.G.A.1
Eng, J.K.2
Hubley, R.3
Vogelzang, M.4
Deutsch, E.W.5
Raught, B.6
Pratt, B.7
Nilsson, E.8
Angeletti, R.H.9
Apweiler, R.10
Cheung, K.11
Costello, C.E.12
Hermjakob, H.13
Huang, S.14
Julian Jr., R.K.15
Kapp, E.16
McComb, M.E.17
Oliver, S.G.18
Omenn, G.19
Paton, N.W.20
Simpson, R.21
Smith, R.22
Taylor, C.F.23
Zhu, W.24
Aebersold, R.25
more..
-
20
-
-
80054018346
-
The ProteoRed MIAPE web toolkit: A user-friendly framework to connect and share proteomics standards
-
Medina-Aunon, J. A., Martinez-Bartolome, S., Lopez-Garcia, M. A., Salazar, E., Navajas, R., Jones, A. R., Paradela, A., and Albar, J. P. (2011) The ProteoRed MIAPE web toolkit: a user-friendly framework to connect and share proteomics standards. Mol Cell Proteomics 10, M111.008334
-
(2011)
Mol Cell Proteomics
, vol.10
-
-
Medina-Aunon, J.A.1
Martinez-Bartolome, S.2
Lopez-Garcia, M.A.3
Salazar, E.4
Navajas, R.5
Jones, A.R.6
Paradela, A.7
Albar, J.P.8
-
21
-
-
48949104656
-
MzML: A single, unifying data format for mass spectrometer output
-
Deutsch, E. (2008) mzML: a single, unifying data format for mass spectrometer output. Proteomics 8, 2776-2777
-
(2008)
Proteomics
, vol.8
, pp. 2776-2777
-
-
Deutsch, E.1
-
22
-
-
78651082595
-
mzML - A community standard for mass spectrometry data
-
Martens, L., Chambers, M., Sturm, M., Kessner, D., Levander, F., Shofstahl, J., Tang, W. H., Rompp, A., Neumann, S., Pizarro, A. D., Montecchi-Palazzi, L., Tasman, N., Coleman, M., Reisinger, F., Souda, P., Hermjakob, H., Binz, P. A., and Deutsch, E. W. (2011) mzML - a community standard for mass spectrometry data. Mol. Cell. Proteomics 10, R110. 000133
-
(2011)
Mol. Cell. Proteomics
, vol.10
-
-
Martens, L.1
Chambers, M.2
Sturm, M.3
Kessner, D.4
Levander, F.5
Shofstahl, J.6
Tang, W.H.7
Rompp, A.8
Neumann, S.9
Pizarro, A.D.10
Montecchi-Palazzi, L.11
Tasman, N.12
Coleman, M.13
Reisinger, F.14
Souda, P.15
Hermjakob, H.16
Binz, P.A.17
Deutsch, E.W.18
-
23
-
-
63849110214
-
MzAPI: A new strategy for efficiently sharing mass spectrometry data
-
Askenazi, M., Parikh, J. R., and Marto, J. A. (2009) mzAPI: a new strategy for efficiently sharing mass spectrometry data. Nat. Methods 6, 240-241
-
(2009)
Nat. Methods
, vol.6
, pp. 240-241
-
-
Askenazi, M.1
Parikh, J.R.2
Marto, J.A.3
-
24
-
-
84856069798
-
mz5: Space- and time-efficient storage of mass spectrometry data sets
-
Wilhelm, M., Kirchner, M., Steen, J. A., and Steen, H. (2011) mz5: space- and time-efficient storage of mass spectrometry data sets. Mol. Cell. Proteomics. 10, O111.011379
-
(2011)
Mol. Cell. Proteomics
, vol.10
-
-
Wilhelm, M.1
Kirchner, M.2
Steen, J.A.3
Steen, H.4
-
25
-
-
4544280727
-
MS1, MS2, and SQT - Three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications
-
DOI 10.1002/rcm.1603
-
McDonald, W. H., Tabb, D. L., Sadygov, R. G., MacCoss, M. J., Venable, J., Graumann, J., Johnson, J. R., Cociorva, D., and Yates, J. R., 3rd (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 (Pubitemid 39222458)
-
(2004)
Rapid Communications in Mass Spectrometry
, vol.18
, Issue.18
, pp. 2162-2168
-
-
McDonald, W.H.1
Tabb, D.L.2
Sadygov, R.G.3
MacCoss, M.J.4
Venable, J.5
Graumann, J.6
Johnson, J.R.7
Cociorva, D.8
Yates III, J.R.9
-
26
-
-
3142702204
-
TANDEM: Matching proteins with tandem mass spectra
-
DOI 10.1093/bioinformatics/bth092
-
Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467 (Pubitemid 38931421)
-
(2004)
Bioinformatics
, vol.20
, Issue.9
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
27
-
-
7044246160
-
Open mass spectrometry search algorithm
-
DOI 10.1021/pr0499491
-
Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., Xu, M., Maynard, D. M., Yang, X., Shi, W., and Bryant, S. H. (2004) Open mass spectrometry search algorithm. J. Proteome Res. 3, 958-964 (Pubitemid 39425651)
-
(2004)
Journal of Proteome Research
, vol.3
, Issue.5
, pp. 958-964
-
-
Geer, L.Y.1
Markey, S.P.2
Kowalak, J.A.3
Wagner, L.4
Xu, M.5
Maynard, D.M.6
Yang, X.7
Shi, W.8
Bryant, S.H.9
-
28
-
-
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
-
29
-
-
0042338362
-
A statistical model for identifying proteins by tandem mass spectrometry
-
DOI 10.1021/ac0341261
-
Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658 (Pubitemid 37082259)
-
(2003)
Analytical Chemistry
, vol.75
, Issue.17
, pp. 4646-4658
-
-
Nesvizhskii, A.I.1
Keller, A.2
Kolker, E.3
Aebersold, R.4
-
30
-
-
33746930864
-
A uniform proteomics MS/MS analysis platform utilizing open XML file formats
-
Keller, A., Eng, J., Zhang, N., Li, X. J., and Aebersold, R. (2005) A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 1, 2005.0017
-
(2005)
Mol. Syst. Biol.
, vol.1
-
-
Keller, A.1
Eng, J.2
Zhang, N.3
Li, X.J.4
Aebersold, R.5
-
31
-
-
84859868686
-
The mzIdentML data standard for mass spectrometry-based proteomics results
-
Jones, A. R., Eisenacher, M., Mayer, G., Kohlbacher, O., Siepen, J., Hubbard, S., Selley, J., Searle, B., Shofstahl, J., Seymour, S., Julian, R., Binz, P. A., Deutsch, E. W., Hermjakob, H., Reisinger, F., Griss, J., Vizcaino, J. A., Chambers, M., Pizarro, A., and Creasy, D. (2012) The mzIdentML data standard for mass spectrometry-based proteomics results. Mol. Cell. Proteomics. 11, M111.014381
-
(2012)
Mol. Cell. Proteomics.
, vol.11
-
-
Jones, A.R.1
Eisenacher, M.2
Mayer, G.3
Kohlbacher, O.4
Siepen, J.5
Hubbard, S.6
Selley, J.7
Searle, B.8
Shofstahl, J.9
Seymour, S.10
Julian, R.11
Binz, P.A.12
Deutsch, E.W.13
Hermjakob, H.14
Reisinger, F.15
Griss, J.16
Vizcaino, J.A.17
Chambers, M.18
Pizarro, A.19
Creasy, D.20
more..
-
32
-
-
18744366090
-
PROTEIOS: An open source proteomics initiative
-
DOI 10.1093/bioinformatics/bti291
-
Garden, P., Alm, R., and Hakkinen, J. (2005) PROTEIOS: an open source proteomics initiative. Bioinformatics 21, 2085-2087 (Pubitemid 40668049)
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 2085-2087
-
-
Garden, P.1
Alm, R.2
Hakkinen, J.3
-
33
-
-
34547141606
-
The PSI formal document process and its implementation on the PSI website
-
DOI 10.1002/pmic.200700064
-
Vizcaino, J. A., Martens, L., Hermjakob, H., Julian, R. K., and Paton, N. W. (2007) The PSI formal document process and its implementation on the PSI website. Proteomics 7, 2355-2357 (Pubitemid 47121527)
-
(2007)
Proteomics
, vol.7
, Issue.14
, pp. 2355-2357
-
-
Vizcaino, J.A.1
Martens, L.2
Hermjakob, H.3
Julian, R.K.4
Paton, N.W.5
-
34
-
-
26844492976
-
A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry
-
DOI 10.1074/mcp.M500141-MCP200
-
Li, X. J., Yi, E. C., Kemp, C. J., Zhang, H., and Aebersold, R. (2005) A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol. Cell. Proteomics 4, 1328-1340 (Pubitemid 41448720)
-
(2005)
Molecular and Cellular Proteomics
, vol.4
, Issue.9
, pp. 1328-1340
-
-
Li, X.-J.1
Yi, E.C.2
Kemp, C.J.3
Zhang, H.4
Aebersold, R.5
-
35
-
-
33747180294
-
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
-
DOI 10.1093/bioinformatics/btl276
-
Bellew, M., Coram, M., Fitzgibbon, M., Igra, M., Randolph, T., Wang, P., May, D., Eng, J., Fang, R., Lin, C., Chen, J., Goodlett, D., Whiteaker, J., Paulovich, A., and McIntosh, M. (2006) A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 22, 1902-1909 (Pubitemid 44283036)
-
(2006)
Bioinformatics
, vol.22
, Issue.15
, pp. 1902-1909
-
-
Bellew, M.1
Coram, M.2
Fitzgibbon, M.3
Igra, M.4
Randolph, T.5
Wang, P.6
May, D.7
Eng, J.8
Fang, R.9
Lin, C.10
Chen, J.11
Goodlett, D.12
Whiteaker, J.13
Paulovich, A.14
McIntosh, M.15
-
36
-
-
35348965139
-
SuperHirn - A novel tool for high resolution LC-MS-based peptide/protein profiling
-
DOI 10.1002/pmic.200700057
-
Mueller, L. N., Rinner, O., Schmidt, A., Letarte, S., Bodenmiller, B., Brusniak, M. Y., Vitek, O., Aebersold, R., and Muller, M. (2007) SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 7, 3470-3480 (Pubitemid 47597670)
-
(2007)
Proteomics
, vol.7
, Issue.19
, pp. 3470-3480
-
-
Mueller, L.N.1
Rinner, O.2
Schmidt, A.3
Letarte, S.4
Bodenmiller, B.5
Brusniak, M.-Y.6
Vitek, O.7
Aebersold, R.8
Muller, M.9
-
37
-
-
62149110095
-
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics
-
Brusniak, M. Y., Bodenmiller, B., Campbell, D., Cooke, K., Eddes, J., Garbutt, A., Lau, H., Letarte, S., Mueller, L. N., Sharma, V., Vitek, O., Zhang, N., Aebersold, R., and Watts, J. D. (2008) Corra: computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics 9, 542
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 542
-
-
Brusniak, M.Y.1
Bodenmiller, B.2
Campbell, D.3
Cooke, K.4
Eddes, J.5
Garbutt, A.6
Lau, H.7
Letarte, S.8
Mueller, L.N.9
Sharma, V.10
Vitek, O.11
Zhang, N.12
Aebersold, R.13
Watts, J.D.14
-
38
-
-
57449099865
-
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
-
Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367-1372
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1367-1372
-
-
Cox, J.1
Mann, M.2
-
39
-
-
33750615386
-
PEPPeR, a platform for experimental proteomic pattern recognition
-
DOI 10.1074/mcp.M600222-MCP200
-
Jaffe, J. D., Mani, D. R., Leptos, K. C., Church, G. M., Gillette, M. A., and Carr, S. A. (2006) PEPPeR, a platform for experimental proteomic pattern recognition. Mol. Cell. Proteomics 5, 1927-1941 (Pubitemid 44688201)
-
(2006)
Molecular and Cellular Proteomics
, vol.5
, Issue.10
, pp. 1927-1941
-
-
Jaffe, J.D.1
Mani, D.R.2
Leptos, K.C.3
Church, G.M.4
Gillette, M.A.5
Carr, S.A.6
-
40
-
-
79955595074
-
MProphet: Automated data processing and statistical validation for large-scale SRM experiments
-
Reiter, L., Rinner, O., Picotti, P., Huttenhain, R., Beck, M., Brusniak, M. Y., Hengartner, M. O., and Aebersold, R. (2011) mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat. Methods 8, 430-435
-
(2011)
Nat. Methods
, vol.8
, pp. 430-435
-
-
Reiter, L.1
Rinner, O.2
Picotti, P.3
Huttenhain, R.4
Beck, M.5
Brusniak, M.Y.6
Hengartner, M.O.7
Aebersold, R.8
-
41
-
-
75749126208
-
Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry
-
Abbatiello, S. E., Mani, D. R., Keshishian, H., and Carr, S. A. (2010) Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry. Clin. Chem. 56, 291-305
-
(2010)
Clin. Chem.
, vol.56
, pp. 291-305
-
-
Abbatiello, S.E.1
Mani, D.R.2
Keshishian, H.3
Carr, S.A.4
-
42
-
-
33947366516
-
Development and validation of a spectral library searching method for peptide identification from MS/MS
-
DOI 10.1002/pmic.200600625
-
Lam, H., Deutsch, E. W., Eddes, J. S., Eng, J. K., King, N., Stein, S. E., and Aebersold, R. (2007) Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7, 655-667 (Pubitemid 46453760)
-
(2007)
Proteomics
, vol.7
, Issue.5
, pp. 655-667
-
-
Lam, H.1
Deutsch, E.W.2
Eddes, J.S.3
Eng, J.K.4
King, N.5
Stein, S.E.6
Aebersold, R.7
-
43
-
-
33747170146
-
Using annotated peptide mass spectrum libraries for protein identification
-
DOI 10.1021/pr0602085
-
Craig, R., Cortens, J. C., Fenyo, D., and Beavis, R. C. (2006) Using annotated peptide mass spectrum libraries for protein identification. J. Proteome Res. 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
-
44
-
-
33747626954
-
Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries
-
DOI 10.1021/ac060279n
-
Frewen, B. E., Merrihew, G. E., Wu, C. C., Noble, W. S., and MacCoss, M. J. (2006) Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal. Chem. 78, 5678-5684 (Pubitemid 44265027)
-
(2006)
Analytical Chemistry
, vol.78
, Issue.16
, pp. 5678-5684
-
-
Frewen, B.E.1
Merrihew, G.E.2
Wu, C.C.3
Noble, W.S.4
MacCoss, M.J.5
-
45
-
-
27544511899
-
InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
-
DOI 10.1021/ac050102d
-
Tanner, S., Shu, H., Frank, A., Wang, L. C., Zandi, E., Mumby, M., Pevzner, P. A., and Bafna, V. (2005) InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 77, 4626-4639 (Pubitemid 41542287)
-
(2005)
Analytical Chemistry
, vol.77
, Issue.14
, pp. 4626-4639
-
-
Tanner, S.1
Shu, H.2
Frank, A.3
Wang, L.-C.4
Zandi, E.5
Mumby, M.6
Pevzner, P.A.7
Bafna, V.8
-
46
-
-
23944526367
-
PRIDE: The proteomics identifications database
-
DOI 10.1002/pmic.200401303
-
Martens, L., Hermjakob, H., Jones, P., Adamski, M., Taylor, C., States, D., Gevaert, K., Vandekerckhove, J., and Apweiler, R. (2005) PRIDE: the proteomics identifications database. Proteomics 5, 3537-3545 (Pubitemid 41192059)
-
(2005)
Proteomics
, vol.5
, Issue.13
, pp. 3537-3545
-
-
Martens, L.1
Hermjakob, H.2
Jones, P.3
Adamsk, M.4
Taylor, C.5
States, D.6
Gevaert, K.7
Vandekerckhove, J.8
Apweiler, R.9
-
47
-
-
67650484732
-
PRIDE Converter: Making proteomics data-sharing easy
-
Barsnes, H., Vizcaino, J. A., Eidhammer, I., and Martens, L. (2009) PRIDE Converter: making proteomics data-sharing easy. Nat. Biotechnol. 27, 598-599
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 598-599
-
-
Barsnes, H.1
Vizcaino, J.A.2
Eidhammer, I.3
Martens, L.4
-
48
-
-
0742323374
-
The HUPO PSI's Molecular Interaction format - A community standard for the representation of protein interaction data
-
DOI 10.1038/nbt926
-
Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., Roechert, B., Poux, S., Jung, E., Mersch, H., Kersey, P., Lappe, M., Li, Y., Zeng, R., Rana, D., Nikolski, M., Husi, H., Brun, C., Shanker, K., Grant, S. G., Sander, C., Bork, P., Zhu, W., Pandey, A., Brazma, A., Jacq, B., Vidal, M., Sherman, D., Legrain, P., Cesareni, G., Xenarios, I., Eisenberg, D., Steipe, B., Hogue, C., and Apweiler, R. (2004) The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Nat. Biotechnol. 22, 177-183 (Pubitemid 38160532)
-
(2004)
Nature Biotechnology
, vol.22
, Issue.2
, pp. 177-183
-
-
Hermjakob, H.1
Montecchi-Palazzi, L.2
Bader, G.3
Wojcik, J.4
Salwinski, L.5
Ceol, A.6
Moore, S.7
Orchard, S.8
Sarkans, U.9
Von Mering, C.10
Roechert, B.11
Poux, S.12
Jung, E.13
Mersch, H.14
Kersey, P.15
Lappe, M.16
Li, Y.17
Zeng, R.18
Rana, D.19
Nikolski, M.20
Husi, H.21
Brun, C.22
Shanker, K.23
Grant, S.G.N.24
Sander, C.25
Bork, P.26
Zhu, W.27
Pandey, A.28
Brazma, A.29
Jacq, B.30
Vidal, M.31
Sherman, D.32
Legrain, P.33
Cesareni, G.34
Xenarios, I.35
Eisenberg, D.36
Steipe, B.37
Hogue, C.38
Apweiler, R.39
more..
-
49
-
-
77956095612
-
Tackling quantitation: A report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea
-
Orchard, S., Jones, A., Albar, J. P., Cho, S. Y., Kwon, K. H., Lee, C., and Hermjakob, H. (2010) Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea. Proteomics 10, 3062-3066
-
(2010)
Proteomics
, vol.10
, pp. 3062-3066
-
-
Orchard, S.1
Jones, A.2
Albar, J.P.3
Cho, S.Y.4
Kwon, K.H.5
Lee, C.6
Hermjakob, H.7
-
50
-
-
77957947158
-
ProHits: Integrated software for mass spectrometry-based interaction proteomics
-
Liu, G., Zhang, J., Larsen, B., Stark, C., Breitkreutz, A., Lin, Z. Y., Breitkreutz, B. J., Ding, Y., Colwill, K., Pasculescu, A., Pawson, T., Wrana, J. L., Nesvizhskii, A. I., Raught, B., Tyers, M., and Gingras, A. C. (2010) ProHits: integrated software for mass spectrometry-based interaction proteomics. Nat. Biotechnol. 28, 1015-1017
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 1015-1017
-
-
Liu, G.1
Zhang, J.2
Larsen, B.3
Stark, C.4
Breitkreutz, A.5
Lin, Z.Y.6
Breitkreutz, B.J.7
Ding, Y.8
Colwill, K.9
Pasculescu, A.10
Pawson, T.11
Wrana, J.L.12
Nesvizhskii, A.I.13
Raught, B.14
Tyers, M.15
Gingras, A.C.16
-
51
-
-
0037163144
-
Design and implementation of Microarray Gene Expression Markup Language (MAGE-ML)
-
RESEARCH0046
-
Spellman, P. T., Miller, M., Stewart, J., Troup, C., Sarkans, U., Chervitz, S., Bernhart, D., Sherlock, G., Ball, C., Lepage, M., Swiatek, M., Marks, W. L., Goncalves, J., Markel, S., Iordan, D., Shojatalab, M., Pizarro, A., White, J., Hubley, R., Deutsch, E., Senger, M., Aronow, B. J., Robinson, A., Bassett, D., Stoeckert, C. J., Jr., and Brazma, A. (2002) Design and implementation of Microarray Gene Expression Markup Language (MAGE-ML). Genome Biol. 3, RESEARCH0046
-
(2002)
Genome Biol.
, vol.3
-
-
Spellman, P.T.1
Miller, M.2
Stewart, J.3
Troup, C.4
Sarkans, U.5
Chervitz, S.6
Bernhart, D.7
Sherlock, G.8
Ball, C.9
Lepage, M.10
Swiatek, M.11
Marks, W.L.12
Goncalves, J.13
Markel, S.14
Iordan, D.15
Shojatalab, M.16
Pizarro, A.17
White, J.18
Hubley, R.19
Deutsch, E.20
Senger, M.21
Aronow, B.J.22
Robinson, A.23
Bassett, D.24
Stoeckert Jr., C.J.25
Brazma, A.26
more..
-
52
-
-
9144232912
-
UniProt: The universal protein knowledgebase
-
Apweiler, R., Bairoch, A., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M. J., Natale, D. A., O'Donovan, C., Redaschi, N., and Yeh, L. S. (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 32, D115-D119 (Pubitemid 38081617)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISS.
-
-
Apweiler, R.1
Bairoch, A.2
Wu, C.H.3
Barker, W.C.4
Boeckmann, B.5
Ferro, S.6
Gasteiger, E.7
Huang, H.8
Lopez, R.9
Magrane, M.10
Martin, M.J.11
Natale, D.A.12
O'Donovan, C.13
Redaschi, N.14
Yeh, L.-S.L.15
-
53
-
-
54949129419
-
ProteoWizard: Open source software for rapid proteomics tools development
-
Kessner, D., Chambers, M., Burke, R., Agus, D., and Mallick, P. (2008) ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24, 2534-2536
-
(2008)
Bioinformatics
, vol.24
, pp. 2534-2536
-
-
Kessner, D.1
Chambers, M.2
Burke, R.3
Agus, D.4
Mallick, P.5
-
54
-
-
84859826519
-
PEAKS DB: De novo sequencing assisted database search for sensitive and accurate peptide identification
-
Zhang, J., Xin, L., Shan, B., Chen, W., Xie, M., Yuen, D., Zhang, W., Zhang, Z., Lajoie, G. A., and Ma, B. (2012) PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification. Mol. Cell. Proteomics 11, M111.010587
-
(2012)
Mol. Cell. Proteomics
, vol.11
-
-
Zhang, J.1
Xin, L.2
Shan, B.3
Chen, W.4
Xie, M.5
Yuen, D.6
Zhang, W.7
Zhang, Z.8
Lajoie, G.A.9
Ma, B.10
-
55
-
-
77949676526
-
A guided tour of the Trans- Proteomic Pipeline
-
Deutsch, E. W., Mendoza, L., Shteynberg, D., Farrah, T., Lam, H., Tasman, N., Sun, Z., Nilsson, E., Pratt, B., Prazen, B., Eng, J. K., Martin, D. B., Nesvizhskii, A. I., and Aebersold, R. (2010) A guided tour of the Trans- Proteomic Pipeline. Proteomics 10, 1150-1159
-
(2010)
Proteomics
, vol.10
, pp. 1150-1159
-
-
Deutsch, E.W.1
Mendoza, L.2
Shteynberg, D.3
Farrah, T.4
Lam, H.5
Tasman, N.6
Sun, Z.7
Nilsson, E.8
Pratt, B.9
Prazen, B.10
Eng, J.K.11
Martin, D.B.12
Nesvizhskii, A.I.13
Aebersold, R.14
-
56
-
-
79952356891
-
Compomics-utilities: An open-source Java library for computational proteomics
-
Barsnes, H., Vaudel, M., Colaert, N., Helsens, K., Sickmann, A., Berven, F. S., and Martens, L. (2011) compomics-utilities: an open-source Java library for computational proteomics. BMC Bioinformatics 12, 70
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 70
-
-
Barsnes, H.1
Vaudel, M.2
Colaert, N.3
Helsens, K.4
Sickmann, A.5
Berven, F.S.6
Martens, L.7
-
57
-
-
84860331423
-
Jmz- Reader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats
-
Griss, J., Reisinger, F., Hermjakob, H., and Vizcaino, J. A. (2012) jmz- Reader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats. Proteomics 12, 795-798
-
(2012)
Proteomics
, vol.12
, pp. 795-798
-
-
Griss, J.1
Reisinger, F.2
Hermjakob, H.3
Vizcaino, J.A.4
-
58
-
-
71749110791
-
Multiplierz: An extensible API based desktop environment for proteomics data analysis
-
Parikh, J. R., Askenazi, M., Ficarro, S. B., Cashorali, T., Webber, J. T., Blank, N. C., Zhang, Y., and Marto, J. A. (2009) multiplierz: an extensible API based desktop environment for proteomics data analysis. BMC Bioinformatics 10, 364
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 364
-
-
Parikh, J.R.1
Askenazi, M.2
Ficarro, S.B.3
Cashorali, T.4
Webber, J.T.5
Blank, N.C.6
Zhang, Y.7
Marto, J.A.8
|