-
1
-
-
38549097071
-
The universal protein resource (uniprot
-
Bairoch, A., Apweiler, R., Wu, C.H., et al. 2008. The Universal Protein Resource (UniProt). Nucleic Acids Res. 35, D190-D195
-
(2008)
Nucleic Acids Res
, vol.35
, pp. D190-D195
-
-
Bairoch, A.1
Apweiler, R.2
Wu, C.H.3
-
2
-
-
34249780156
-
Shotgun protein sequencing: Assembly of peptide tandem mass spectra from mixtures of modified proteins
-
Bandeira, N., Clauser, K.R., and Pevzner, P.A. 2007a. Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Mol. Cell. Proteomics 6, 1123-1134
-
(2007)
Mol. Cell. Proteomics
, vol.6
, pp. 1123-1134
-
-
Bandeira, N.1
Clauser, K.R.2
Pevzner, P.A.3
-
3
-
-
10644292740
-
Shotgun protein sequencing by tandem mass spectra assembly
-
Bandeira, N., Tang, H., Bafna, V., et al. 2004. Shotgun protein sequencing by tandem mass spectra assembly. Anal. Chem. 76, 7221-7233
-
(2004)
Anal. Chem
, vol.76
, pp. 7221-7233
-
-
Bandeira, N.1
Tang, H.2
Bafna, V.3
-
4
-
-
34249826390
-
Protein identification by spectral networks analysis
-
Bandeira, N., Tsur, D., Frank, A., et al. 2007b. Protein identification by spectral networks analysis. Proc. Natl. Acad. Sci. USA 104, 6140-6145
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 6140-6145
-
-
Bandeira, N.1
Tsur, D.2
Frank, A.3
-
7
-
-
58549101102
-
Discovery and revision of arabidopsis genes by proteogenomics
-
Castellana, N.E., Payne, S.H., Shen, Z., et al. 2008. Discovery and revision of Arabidopsis genes by proteogenomics. Proc. Natl. Acad. Sci. USA 105, 21034-21038
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 21034-21038
-
-
Castellana, N.E.1
Payne, S.H.2
Shen, Z.3
-
8
-
-
84885043595
-
Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site
-
Chourey, K., Nissen, S., Vishnivetskaya, T., et al. 2013. Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- And nitrate-contaminated site. Proteomics 13, 2921-2930
-
(2013)
Proteomics
, vol.13
, pp. 2921-2930
-
-
Chourey, K.1
Nissen, S.2
Vishnivetskaya, T.3
-
10
-
-
3142702204
-
Tandem: Matching proteins with tandem mass spectra
-
Craig, R., and Beavis, R.C. 2004. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467
-
(2004)
Bioinformatics
, vol.20
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
11
-
-
0032750293
-
De novo peptide sequencing via tandem mass spectrometry
-
Dancík, V., Addona, T.A., Clauser, K.R., et al. 1999. De novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol. 6, 327-342
-
(1999)
J. Comput. Biol
, vol.6
, pp. 327-342
-
-
Dancík, V.1
Addona, T.A.2
Clauser, K.R.3
-
12
-
-
84855544582
-
Strong cation exchange chromatography in analysis of posttranslational modifications: Innovations and perspectives
-
Edelmann, M.J. 2011. Strong cation exchange chromatography in analysis of posttranslational modifications: innovations and perspectives. J. Biomed. Biotechnol. 2011, 1-7
-
(2011)
J. Biomed. Biotechnol
, vol.2011
, pp. 1-7
-
-
Edelmann, M.J.1
-
13
-
-
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
-
14
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng, J.K., McCormack, A.L., and Yates, J.R. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989
-
(1994)
J. Am. Soc. Mass Spectrom
, vol.5
, pp. 976-989
-
-
Eng, J.K.1
McCormack, A.L.2
Yates, J.R.3
-
15
-
-
38649109810
-
Clustering millions of tandem mass spectra
-
Frank, A.M., Bandeira, N., Shen, Z., et al. 2008. Clustering millions of tandem mass spectra. J. Proteome Res. 7, 113-122
-
(2008)
J. Proteome Res
, vol.7
, pp. 113-122
-
-
Frank, A.M.1
Bandeira, N.2
Shen, Z.3
-
16
-
-
33846600820
-
De novo peptide sequencing and identification with precision mass spectrometry
-
Frank, A.M., Savitski, M.M., Nielsen, M.L., et al. 2007. De novo peptide sequencing and identification with precision mass spectrometry. J. Proteome Res. 6, 114-123
-
(2007)
J. Proteome Res
, vol.6
, pp. 114-123
-
-
Frank, A.M.1
Savitski, M.M.2
Nielsen, M.L.3
-
17
-
-
79959960525
-
Target-decoy approach and false discovery rate: When things may go wrong
-
Gupta, N., Bandeira, N., Keich, U., et al. 2011. Target-decoy approach and false discovery rate: when things may go wrong. J. Am. Soc. Mass Spectrom. 22, 1111-1120
-
(2011)
J. Am. Soc. Mass Spectrom
, vol.22
, pp. 1111-1120
-
-
Gupta, N.1
Bandeira, N.2
Keich, U.3
-
18
-
-
84865737357
-
Peptide identification by tandem mass spectrometry with alternate fragmentation modes
-
Guthals, A., and Bandeira, N. 2012. Peptide identification by tandem mass spectrometry with alternate fragmentation modes. Mol. Cell. Proteomics 11, 550-557
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 550-557
-
-
Guthals, A.1
Bandeira, N.2
-
19
-
-
84867161019
-
Shotgun protein sequencing with meta-contig assembly
-
Guthals, A., Clauser, K.R., and Bandeira, N. 2012a. Shotgun protein sequencing with meta-contig assembly. Mol. Cell. Proteomics 10, 1084-1096
-
(2012)
Mol. Cell. Proteomics
, vol.10
, pp. 1084-1096
-
-
Guthals, A.1
Clauser, K.R.2
Bandeira, N.3
-
20
-
-
84879399812
-
Sequencing-grade de novo analysis of ms/ms triplets (cid/hcd/.etd) from overlapping peptides
-
Guthals, A., Clauser, K.R., Frank, A.M., et al. 2013. Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/.ETD) from overlapping peptides. J. Proteome Res. 12, 2846-2857
-
(2013)
J. Proteome Res
, vol.12
, pp. 2846-2857
-
-
Guthals, A.1
Clauser, K.R.2
Frank, A.M.3
-
21
-
-
84865766850
-
The spectral networks paradigm in high throughput mass spectrometry
-
Guthals, A., Watrous, J.D., Dorrestein, P.C., et al. 2012b. The spectral networks paradigm in high throughput mass spectrometry. Mol. Biosyst. 8, 2535-2544
-
(2012)
Mol. Biosyst
, vol.8
, pp. 2535-2544
-
-
Guthals, A.1
Watrous, J.D.2
Dorrestein, P.C.3
-
22
-
-
84859984784
-
Deep metaproteomic analysis of human salivary supernatant
-
Jagtap, P., McGowan, T., Bandhakavi, S., et al. 2012. Deep metaproteomic analysis of human salivary supernatant. Proteomics 12, 992-1001
-
(2012)
Proteomics
, vol.12
, pp. 992-1001
-
-
Jagtap, P.1
McGowan, T.2
Bandhakavi, S.3
-
23
-
-
84878045698
-
False discovery rates in spectral identification
-
Jeong, K., Kim, S., and Bandeira, N. 2012. False discovery rates in spectral identification. BMC Bioinformatics 13 Suppl 1, S2
-
(2012)
BMC Bioinformatics
, vol.13
, pp. S2
-
-
Jeong, K.1
Kim, S.2
Bandeira, N.3
-
24
-
-
54949129419
-
Proteowizard: Open source software for rapid proteomics tools development
-
Kessner, D., Chambers, M., Burke, R., et al. 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
-
25
-
-
50149117169
-
Spectral probabilities and generating functions of tandem mass spectra: A strike against decoy databases
-
Kim, S., Gupta, N., and Pevzner, P.A. 2008. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J. Proteome Res. 7, 3354-3363
-
(2008)
J. Proteome Res
, vol.7
, pp. 3354-3363
-
-
Kim, S.1
Gupta, N.2
Pevzner, P.A.3
-
26
-
-
78650147228
-
The generating function of cid etd, and cid/etd pairs of tandem mass spectra: Applications to database search
-
Kim, S., Mischerikow, N., Bandeira, N., et al. 2010. The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. Mol. Cell. Proteomics 9, 2840-2852
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 2840-2852
-
-
Kim, S.1
Mischerikow, N.2
Bandeira, N.3
-
27
-
-
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. Proteomics 73, 2092-2123
-
(2010)
J. Proteomics
, vol.73
, pp. 2092-2123
-
-
Nesvizhskii, A.I.1
-
28
-
-
0033434080
-
Probability-based protein identification by searching sequence databases using mass spectrometry data
-
Perkins, D.N., Pappin, D.J., Creasy, D.M., et al. 1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567
-
(1999)
Electrophoresis
, vol.20
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.2
Creasy, D.M.3
-
29
-
-
0034915775
-
Mutation-Tolerant protein identification by mass spectrometry
-
Pevzner, P.A., Dancík, V., and Tang, C.L. 2000. Mutation-Tolerant protein identification by mass spectrometry. J. Comput. Biol. 7, 777-787
-
(2000)
J. Comput. Biol
, vol.7
, pp. 777-787
-
-
Pevzner, P.A.1
Dancík, V.2
Tang, C.L.3
-
30
-
-
77949786295
-
Value of using multiple proteases for large-scale mass spectrometrybased proteomics
-
Swaney, D.L., Wenger, C.D., and Coon, J.J. 2010. Value of using multiple proteases for large-scale mass spectrometrybased proteomics. J. Proteome Res. 9, 1323-1329
-
(2010)
J. Proteome Res
, vol.9
, pp. 1323-1329
-
-
Swaney, D.L.1
Wenger, C.D.2
Coon, J.J.3
-
31
-
-
0037953090
-
Similarity among tandem mass spectra from proteomic experiments: Detection, significance, and utility
-
Tabb, D.L., MacCoss, M.J., Wu, C.C., et al. 2003. Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal. Chem. 75, 2470-2477
-
(2003)
Anal. Chem
, vol.75
, pp. 2470-2477
-
-
Tabb, D.L.1
MacCoss, M.J.2
Wu, C.C.3
|