-
1
-
-
0035142375
-
Genomic sequence of hyperthermophile, Pyrococcus furiosus: Implications for physiology and enzymology
-
Robb, F. T.; Maeder, D. L.; Brown, J. R.; DiRuggiero, J.; Stump, M. D.; Yeh, R. K.; Weiss, R. B.; Dunn, D. M. Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology Methods Enzymol. 2001, 330, 134-57
-
(2001)
Methods Enzymol.
, vol.330
, pp. 134-157
-
-
Robb, F.T.1
Maeder, D.L.2
Brown, J.R.3
Diruggiero, J.4
Stump, M.D.5
Yeh, R.K.6
Weiss, R.B.7
Dunn, D.M.8
-
2
-
-
0041884952
-
Identification of 2D-gel proteins: A comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry
-
Lim, H.; Eng, J.; Yates, J. R., III; Tollaksen, S. L.; Giometti, C. S.; Holden, J. F.; Adams, M. W.; Reich, C. I.; Olsen, G. J.; Hays, L. G. Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu 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, J.R.3
Tollaksen, S.L.4
Giometti, C.S.5
Holden, J.F.6
Adams, M.W.7
Reich, C.I.8
Olsen, G.J.9
Hays, L.G.10
-
3
-
-
0035163296
-
Identification of membrane proteins in the hyperthermophilic archaeon Pyrococcus furiosus using proteomics and prediction programs
-
Holden, J. F.; Poole, F. L., Jr.; Tollaksen, S. L.; Giometti, C. S.; Lim, H.; Yates, J. R., III; Adams, M. W. W. Identification of membrane proteins in the hyperthermophilic archaeon Pyrococcus furiosus using proteomics and prediction programs Comp. Funct. Genomics 2001, 2, 275-88
-
(2001)
Comp. Funct. Genomics
, vol.2
, pp. 275-288
-
-
Holden, J.F.1
Poole, Jr.F.L.2
Tollaksen, S.L.3
Giometti, C.S.4
Lim, H.5
Yates III, J.R.6
Adams, M.W.W.7
-
4
-
-
68549136910
-
Proteomics of Pyrococcus furiosus, a hyperthermophilic archaeon refractory to traditional methods
-
Lee, A. M.; Sevinsky, J. R.; Bundy, J. L.; Grunden, A. M.; Stephenson, J. L., Jr. Proteomics of Pyrococcus furiosus, a hyperthermophilic archaeon refractory to traditional methods J. Proteome Res. 2009, 8, 3844-51
-
(2009)
J. Proteome Res.
, vol.8
, pp. 3844-3851
-
-
Lee, A.M.1
Sevinsky, J.R.2
Bundy, J.L.3
Grunden, A.M.4
Stephenson, Jr.J.L.5
-
5
-
-
0011970033
-
Peptide sequence analysis on quadrupole mass spectrometers
-
McCormack, A. L.; Eng, J. K.; Yates, J. R., III. Peptide sequence analysis on quadrupole mass spectrometers Methods: A Companion to Methods in Enzymology 1994, 6, 274-273
-
(1994)
Methods: A Companion to Methods in Enzymology
, vol.6
, pp. 274-273
-
-
McCormack, A.L.1
Eng, J.K.2
Yates III, J.R.3
-
6
-
-
0031568420
-
Direct analysis and identification of proteins in mixtures by LC-MS/MS and database searching at the low-femtomole level
-
McCormack, A. L.; Schieltz, D. M.; Goode, B.; Yang, S.; Barnes, G.; Drubin, D.; Yates, J. R., III. Direct analysis and identification of proteins in mixtures by LC-MS/MS and database searching at the low-femtomole level Anal. Chem. 1997, 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
-
7
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng, J.; McCormack, A.; Yates, J. 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, J.1
McCormack, A.2
Yates, J.3
-
8
-
-
1842681979
-
Standard mixtures for proteome studies
-
Purvine, S.; Picone, A. F.; Kolker, E. Standard mixtures for proteome studies OMICS 2004, 8, 79-92
-
(2004)
OMICS
, vol.8
, pp. 79-92
-
-
Purvine, S.1
Picone, A.F.2
Kolker, E.3
-
9
-
-
0036406762
-
Experimental protein mixture for validating tandem mass spectral analysis
-
Keller, A.; Purvine, S.; Nesvizhskii, A. I.; Stolyar, S.; Goodlett, D. R.; Kolker, E. Experimental protein mixture for validating tandem mass spectral analysis OMICS 2002, 6, 207-12
-
(2002)
OMICS
, vol.6
, pp. 207-212
-
-
Keller, A.1
Purvine, S.2
Nesvizhskii, A.I.3
Stolyar, S.4
Goodlett, D.R.5
Kolker, E.6
-
10
-
-
67349196123
-
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
-
Bell, A. W.; Deutsch, E. W.; Au, C. E.; Kearney, R. E.; Beavis, R.; Sechi, S.; Nilsson, T.; Bergeron, J. J. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics Nat. Methods 2009, 6, 423-30
-
(2009)
Nat. Methods
, vol.6
, pp. 423-430
-
-
Bell, A.W.1
Deutsch, E.W.2
Au, C.E.3
Kearney, R.E.4
Beavis, R.5
Sechi, S.6
Nilsson, T.7
Bergeron, J.J.8
-
11
-
-
0033051101
-
Direct analysis of protein complexes using mass spectrometry
-
Link, A. J.; Eng, J.; Schieltz, D. M.; Carmack, E.; Mize, G. J.; Morris, D. R.; Garvik, B. M.; Yates, J. R., III. Direct analysis of protein complexes using mass spectrometry Nat. Biotechnol. 1999, 17, 676-82
-
(1999)
Nat. Biotechnol.
, vol.17
, pp. 676-682
-
-
Link, A.J.1
Eng, J.2
Schieltz, D.M.3
Carmack, E.4
Mize, G.J.5
Morris, D.R.6
Garvik, B.M.7
Yates III, J.R.8
-
12
-
-
0035106351
-
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
-
Washburn, M. P.; Wolters, D.; Yates, J. R., III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nat. Biotechnol. 2001, 19, 242-7
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 242-247
-
-
Washburn, M.P.1
Wolters, D.2
Yates III, J.R.3
-
13
-
-
84988119833
-
The use of bacteriophage T4 as a set of molecular weight and isoelectric point markers for two-dimensional electrophoresis
-
Ponnamma Kurian, D. M. G.; Suhocki, P. V.; Ledley, G. The use of bacteriophage T4 as a set of molecular weight and isoelectric point markers for two-dimensional electrophoresis Electrophoresis 2005, 2, 184-187
-
(2005)
Electrophoresis
, vol.2
, pp. 184-187
-
-
Ponnamma Kurian, D.M.G.1
Suhocki, P.V.2
Ledley, G.3
-
14
-
-
13844316454
-
Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations
-
Kolker, E.; Picone, A. F.; Galperin, M. Y.; Romine, M. F.; Higdon, R.; Makarova, K. S.; Kolker, N.; Anderson, G. A.; Qiu, X.; Auberry, K. J.; Babnigg, G.; Beliaev, A. S.; Edlefsen, P.; Elias, D. A.; Gorby, Y. A.; Holzman, T.; Klappenbach, J. A.; Konstantinidis, K. T.; Land, M. L.; Lipton, M. S.; McCue, L. A.; Monroe, M.; Pasa-Tolic, L.; Pinchuk, G.; Purvine, S.; Serres, M. H.; Tsapin, S.; Zakrajsek, B. A.; Zhu, W.; Zhou, J.; Larimer, F. W.; Lawrence, C. E.; Riley, M.; Collart, F. R.; Yates, J. R., III; Smith, R. D.; Giometti, C. S.; Nealson, K. H.; Fredrickson, J. K.; Tiedje, J. M. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2099-104
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 2099-2104
-
-
Kolker, E.1
Picone, A.F.2
Galperin, M.Y.3
Romine, M.F.4
Higdon, R.5
Makarova, K.S.6
Kolker, N.7
Anderson, G.A.8
Qiu, X.9
Auberry, K.J.10
Babnigg, G.11
Beliaev, A.S.12
Edlefsen, P.13
Elias, D.A.14
Gorby, Y.A.15
Holzman, T.16
Klappenbach, J.A.17
Konstantinidis, K.T.18
Land, M.L.19
Lipton, M.S.20
McCue, L.A.21
Monroe, M.22
Pasa-Tolic, L.23
Pinchuk, G.24
Purvine, S.25
Serres, M.H.26
Tsapin, S.27
Zakrajsek, B.A.28
Zhu, W.29
Zhou, J.30
Larimer, F.W.31
Lawrence, C.E.32
Riley, M.33
Collart, F.R.34
Yates III, J.R.35
Smith, R.D.36
Giometti, C.S.37
Nealson, K.H.38
Fredrickson, J.K.39
Tiedje, J.M.40
more..
-
15
-
-
0035143450
-
Pyrococcus furiosus: Large-scale cultivation and enzyme purification
-
Verhagen, M. F.; Menon, A. L.; Schut, G. J.; Adams, M. W. Pyrococcus furiosus: large-scale cultivation and enzyme purification Methods Enzymol. 2001, 330, 25-30
-
(2001)
Methods Enzymol.
, vol.330
, pp. 25-30
-
-
Verhagen, M.F.1
Menon, A.L.2
Schut, G.J.3
Adams, M.W.4
-
16
-
-
30744476222
-
Performance of a linear ion trap-Orbitrap hybrid for peptide analysis
-
Yates, J. R.; Cociorva, D.; Liao, L.; Zabrouskov, V. Performance of a linear ion trap-Orbitrap hybrid for peptide analysis Anal. Chem. 2006, 78, 493-500
-
(2006)
Anal. Chem.
, vol.78
, pp. 493-500
-
-
Yates, J.R.1
Cociorva, D.2
Liao, L.3
Zabrouskov, V.4
-
17
-
-
57049106891
-
An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures
-
Schmidt, A.; Gehlenborg, N.; Bodenmiller, B.; Mueller, L. N.; Campbell, D.; Mueller, M.; Aebersold, R.; Domon, B. An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures Mol. Cell. Proteomics 2008, 7 (11) 2138-50
-
(2008)
Mol. Cell. Proteomics
, vol.7
, Issue.11
, pp. 2138-2150
-
-
Schmidt, A.1
Gehlenborg, N.2
Bodenmiller, B.3
Mueller, L.N.4
Campbell, D.5
Mueller, M.6
Aebersold, R.7
Domon, B.8
-
18
-
-
35348965139
-
SuperHirn: A novel tool for high resolution LC-MS-based peptide/protein profiling
-
Mueller, L. N.; Rinner, O.; Schmidt, A.; Letarte, S.; Bodenmiller, B.; Brusniak, M. Y.; Vitek, O.; Aebersold, R.; Muller, M. SuperHirn: a novel tool for high resolution LC-MS-based peptide/protein profiling Proteomics 2007, 7 (19) 3470-80
-
(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
-
19
-
-
0029644596
-
Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database
-
Yates, J. R., III; Eng, J. K.; McCormack, A. L.; Schieltz, D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database Anal. Chem. 1995, 67 (8) 1426-36
-
(1995)
Anal. Chem.
, vol.67
, Issue.8
, pp. 1426-1436
-
-
Iii R., Y.J.1
Eng, J.K.2
McCormack, A.L.3
Schieltz, D.4
-
20
-
-
0037108887
-
Empirical statistical model to estimate the accuracy of peptide identification made by MS/MS and database search
-
Keller, A.; Nesvizhskii, A.; Kolder, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identification made by MS/MS and database search Anal. Chem. 2002, 74 (20) 5383-92
-
(2002)
Anal. Chem.
, vol.74
, Issue.20
, pp. 5383-5392
-
-
Keller, A.1
Nesvizhskii, A.2
Kolder, E.3
Aebersold, R.4
-
21
-
-
0042338362
-
A statistical model for identifying proteins by tandem mass specrometry
-
Nesvizhskii, A.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass specrometry Anal. Chem. 2002, 75 (17) 4646-58
-
(2002)
Anal. Chem.
, vol.75
, Issue.17
, pp. 4646-4658
-
-
Nesvizhskii, A.1
Keller, A.2
Kolker, E.3
Aebersold, R.4
-
22
-
-
33750631580
-
Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis
-
Hoerth, P.; Miller, C. A.; Preckel, T.; Wenz, C. Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis Mol. Cell. Proteomics. 2006, 5, 1968-1974
-
(2006)
Mol. Cell. Proteomics.
, vol.5
, pp. 1968-1974
-
-
Hoerth, P.1
Miller, C.A.2
Preckel, T.3
Wenz, C.4
-
23
-
-
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.; Tabb, D. L.; Sadygov, R. G.; MacCoss, M. J.; Venable, J.; Graumann, J.; Johnson, J. R.; Cociorva, D.; Yates, J. R., III. 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. 2004, 18, 2162-8
-
(2004)
Rapid Commun. Mass Spectrom.
, vol.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
-
24
-
-
0037277179
-
Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome
-
Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome J. Proteome Res. 2003, 2, 43-50
-
(2003)
J. Proteome Res.
, vol.2
, pp. 43-50
-
-
Peng, J.1
Elias, J.E.2
Thoreen, C.C.3
Licklider, L.J.4
Gygi, S.P.5
-
25
-
-
35648943746
-
ProLuCID, a fast and sensitive tandem mass spectra-based protein identification program
-
Xu, T.; Park, V. J.; Cociorva, S. K.; Lu, D.; Liao, B.; Wohlschlegel, L.; Hewel, J.; J, Yates, J. R., III. ProLuCID, a fast and sensitive tandem mass spectra-based protein identification program Mol. Cell. Proteomics 2006, 5, S174-S174
-
(2006)
Mol. Cell. Proteomics
, vol.5
-
-
Xu, T.1
Park, V.J.2
Cociorva, S.K.3
Lu, D.4
Liao, B.5
Wohlschlegel, L.6
Hewel, J.7
Yates III, J.R.8
-
26
-
-
43349089502
-
Validation of Tandem Mass Spectrometry Database Search Results Using DTASelect
-
In; WIley: New York, Chapter 13.
-
Cociorva, D.; Tabb, D. L.; Yates, J. R., III. Validation of Tandem Mass Spectrometry Database Search Results Using DTASelect. In Current Protocols in Bioinformatics; WIley: New York, 2007; Chapter 13.
-
(2007)
Current Protocols in Bioinformatics
-
-
Cociorva, D.1
Tabb, D.L.2
Yates III, J.R.3
-
27
-
-
3242731195
-
A model for random sampling and estimation of relative protein abundance in shotgun proteomics
-
Liu, H.; Sadygov, R. G.; Yates, J. R., III. A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal. Chem. 2004, 76, 4193-201
-
(2004)
Anal. Chem.
, vol.76
, pp. 4193-4201
-
-
Liu, H.1
Sadygov, R.G.2
Yates III, J.R.3
-
28
-
-
3543023287
-
Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture
-
Durr, E.; Yu, J.; Krasinska, K. M.; Carver, L. A.; Yates, J. R.; Testa, J. E.; Oh, P.; Schnitzer, J. E. Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture Nat. Biotechnol. 2004, 22, 985-92
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 985-992
-
-
Durr, E.1
Yu, J.2
Krasinska, K.M.3
Carver, L.A.4
Yates, J.R.5
Testa, J.E.6
Oh, P.7
Schnitzer, J.E.8
|