-
1
-
-
33751340274
-
Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics
-
10.1039/b610957h 17124542
-
Hendrickson EL Xia Q Wang T Leigh JA Hackett M Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics Analyst 2006, 131(12):1335-1341. 10.1039/b610957h 17124542
-
(2006)
Analyst
, vol.131
, Issue.12
, pp. 1335-1341
-
-
Hendrickson, E.L.1
Xia, Q.2
Wang, T.3
Leigh, J.A.4
Hackett, M.5
-
2
-
-
33646927488
-
Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR
-
10.1074/mcp.M500369-MCP200 16489187
-
Xia Q: Hendrickson EL Zhang Y Wang T Taub F Moore BC Porat I Whitman WB Hackett M Leigh JA Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR Mol Cell Proteomics 2006, 5(5):868-881. 10.1074/mcp.M500369-MCP200 16489187
-
(2006)
Mol Cell Proteomics
, vol.5
, Issue.5
, pp. 868-881
-
-
Xia, Q.1
Hendrickson, E.L.2
Zhang, Y.3
Wang, T.4
Taub, F.5
Moore, B.C.6
Porat, I.7
Whitman, W.B.8
Hackett, M.9
Leigh, J.A.10
-
3
-
-
34547830828
-
Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: Application to mass spec data
-
10.1093/bioinformatics/btm130 17459967
-
Park Y Downing SR Kim D Hahn WC Li C Kantoff PW Wei LJ Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: Application to mass spec data Bioinformatics 2007, 23(12):1451-1458. 10.1093/bioinformatics/btm130 17459967
-
(2007)
Bioinformatics
, vol.23
, Issue.12
, pp. 1451-1458
-
-
Park, Y.1
Downing, S.R.2
Kim, D.3
Hahn, W.C.4
Li, C.5
Kantoff, P.W.6
Wei, L.J.7
-
4
-
-
33750080170
-
ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis
-
10.1016/j.tube.2005.10.002 16376151
-
Cho SH Goodlett D Franzblau S ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis Tuberculosis (Edinb) 2006, 86(6):445-460. 10.1016/j.tube.2005.10.002 16376151
-
(2006)
Tuberculosis (Edinb)
, vol.86
, Issue.6
, pp. 445-460
-
-
Cho, S.H.1
Goodlett, D.2
Franzblau, S.3
-
5
-
-
33847369414
-
Quantitative proteomic and microarray analysis of the archaeon Methanosarcina acetivorans grown with acetate versus methanol
-
10.1021/pr060383l 17269732
-
Li L Li Q Rohlin L Kim U Salmon K Rejtar T Gunsalus RP Karger BL Ferry JG Quantitative proteomic and microarray analysis of the archaeon Methanosarcina acetivorans grown with acetate versus methanol J Proteome Res 2007, 6(2):759-771. 10.1021/pr060383l 17269732
-
(2007)
J Proteome Res
, vol.6
, Issue.2
, pp. 759-771
-
-
Li, L.1
Li, Q.2
Rohlin, L.3
Kim, U.4
Salmon, K.5
Rejtar, T.6
Gunsalus, R.P.7
Karger, B.L.8
Ferry, J.G.9
-
6
-
-
18144406113
-
Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry
-
10.1021/ac048204b 15859588
-
Molina H Parmigiani G Pandey A Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry Anal Chem 2005, 77(9):2739-2744. 10.1021/ac048204b 15859588
-
(2005)
Anal Chem
, vol.77
, Issue.9
, pp. 2739-2744
-
-
Molina, H.1
Parmigiani, G.2
Pandey, A.3
-
7
-
-
33745828376
-
Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profiles
-
10.1021/pr050436j 16823959
-
Piening BD Wang P Bangur CS Whiteaker J Zhang H Feng LC Keane JF Eng JK Tang H Prakash A McIntosh MW Paulovich A Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profiles J Proteome Res 2006, 5(7):1527-1534. 10.1021/ pr050436j 16823959
-
(2006)
J Proteome Res
, vol.5
, Issue.7
, pp. 1527-1534
-
-
Piening, B.D.1
Wang, P.2
Bangur, C.S.3
Whiteaker, J.4
Zhang, H.5
Feng, L.C.6
Keane, J.F.7
Eng, J.K.8
Tang, H.9
Prakash, A.10
McIntosh, M.W.11
Paulovich, A.12
-
8
-
-
33846410247
-
Quantitative analysis of complex peptide mixtures using FTMS and differential mass spectrometry
-
10.1016/j.jasms.2006.09.014 17070068
-
Meng F Wiener MC Sachs JR Burns C Verma P Paweletz CP Mazur MT Deyanova EG Yates NA Hendrickson RC Quantitative analysis of complex peptide mixtures using FTMS and differential mass spectrometry J Am Soc Mass Spectrom 2007, 18(2):226-233. 10.1016/j.jasms.2006.09.014 17070068
-
(2007)
J Am Soc Mass Spectrom
, vol.18
, Issue.2
, pp. 226-233
-
-
Meng, F.1
Wiener, M.C.2
Sachs, J.R.3
Burns, C.4
Verma, P.5
Paweletz, C.P.6
Mazur, M.T.7
Deyanova, E.G.8
Yates, N.A.9
Hendrickson, R.C.10
-
9
-
-
34250898652
-
A new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS
-
10.1021/pr0606880 17441747
-
Andreev VP Li L Cao L Gu Y Rejtar T Wu SL Karger BL A new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS J Proteome Res 2007, 6(6):2186-2194. 10.1021/pr0606880 17441747
-
(2007)
J Proteome Res
, vol.6
, Issue.6
, pp. 2186-2194
-
-
Andreev, V.P.1
Li, L.2
Cao, L.3
Gu, Y.4
Rejtar, T.5
Wu, S.L.6
Karger, B.L.7
-
10
-
-
33747197432
-
New algorithm for 15N/14N quantitation with LC-ESI-MS using an LTQ-FT mass spectrometer
-
10.1021/pr060105m 16889428
-
Andreev VP Li L Rejtar T Li Q Ferry JG Karger BL New algorithm for 15N/ 14N quantitation with LC-ESI-MS using an LTQ-FT mass spectrometer J Proteome Res 2006, 5(8):2039-2045. 10.1021/pr060105m 16889428
-
(2006)
J Proteome Res
, vol.5
, Issue.8
, pp. 2039-2045
-
-
Andreev, V.P.1
Li, L.2
Rejtar, T.3
Li, Q.4
Ferry, J.G.5
Karger, B.L.6
-
11
-
-
34547746723
-
Reproducibility assessment of relative quantitation strategies for LC-MS based proteomics
-
10.1021/ac070200u 17580949
-
Kim YJ Zhan P Feild B Ruben SM He T Reproducibility assessment of relative quantitation strategies for LC-MS based proteomics Anal Chem 2007, 79(15):5651-5658. 10.1021/ac070200u 17580949
-
(2007)
Anal Chem
, vol.79
, Issue.15
, pp. 5651-5658
-
-
Kim, Y.J.1
Zhan, P.2
Feild, B.3
Ruben, S.M.4
He, T.5
-
12
-
-
17844394177
-
Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry
-
10.1074/mcp.R500005-MCP200 15741312
-
Listgarten J Emili A Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry Mol Cell Proteomics 2005, 4(4):419-434. 10.1074/ mcp.R500005-MCP200 15741312
-
(2005)
Mol Cell Proteomics
, vol.4
, Issue.4
, pp. 419-434
-
-
Listgarten, J.1
Emili, A.2
-
13
-
-
33846817288
-
Global and targeted quantitative proteomics for biomarker discovery
-
10.1016/j.jchromb.2006.09.004 17023222
-
Veenstra TD Global and targeted quantitative proteomics for biomarker discovery J Chromatogr B Analyt Technol Biomed Life Sci 2007, 847(1):3-11. 10.1016/j.jchromb.2006.09.004 17023222
-
(2007)
J Chromatogr B Analyt Technol Biomed Life Sci
, vol.847
, Issue.1
, pp. 3-11
-
-
Veenstra, T.D.1
-
14
-
-
33646564676
-
Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes
-
10.1021/pr050406g 16674111
-
Wang G Wu WW Zeng W Chou CL Shen RF Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes J Proteome Res 2006, 5(5):1214-1223. 10.1021/pr050406g 16674111
-
(2006)
J Proteome Res
, vol.5
, Issue.5
, pp. 1214-1223
-
-
Wang, G.1
Wu, W.W.2
Zeng, W.3
Chou, C.L.4
Shen, R.F.5
-
15
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
33173 11309499 10.1073/pnas.091062498
-
Tusher VG Tibshirani R Chu G Significance analysis of microarrays applied to the ionizing radiation response Proc Natl Acad Sci U S A 2001, 98(9):5116-5121. 33173 11309499 10.1073/pnas.091062498
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, Issue.9
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
16
-
-
33745591083
-
Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system
-
1779535 16784548 10.1186/gb-2006-7-6-r50
-
de Godoy LM Olsen JV de Souza GA Li G Mortensen P Mann M Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system Genome Biol 2006 7(6):R50. 1779535 16784548 10.1186/ gb-2006-7-6-r50
-
(2006)
Genome Biol
, vol.7
, Issue.6
-
-
de Godoy, L.M.1
Olsen, J.V.2
de Souza, G.A.3
Li, G.4
Mortensen, P.5
Mann, M.6
-
17
-
-
0345822598
-
The positive discovery rate: A Bayesian interpretation and the q-value
-
10.1214/aos/1074290335
-
Storey JD The positive discovery rate: A Bayesian interpretation and the q-value The Annuals of statistics 2003, 31(6):2013-2035. 10.1214/aos/ 1074290335
-
(2003)
The Annuals of Statistics
, vol.31
, Issue.6
, pp. 2013-2035
-
-
Storey, J.D.1
-
18
-
-
3242731195
-
A model for random sampling and estimation of relative protein abundance in shotgun proteomics
-
10.1021/ac0498563 15253663
-
Liu H Sadygov RG Yates JR 3rd A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal Chem 2004, 76(14):4193-4201. 10.1021/ac0498563 15253663
-
(2004)
Anal Chem
, vol.76
, Issue.14
, pp. 4193-4201
-
-
Liu, H.1
Sadygov, R.G.2
Yates III, J.R.3
-
19
-
-
33747172505
-
Application of the accurate mass and time tag approach to the proteome analysis of sub-cellular fractions obtained from Rhodobacter sphaeroides 2.4.1. Aerobic and photosynthetic cell cultures
-
10.1021/pr060050o 16889416
-
Callister SJ Dominguez MA Nicora CD Zeng X Tavano CL Kaplan S Donohue TJ Smith RD Lipton MS Application of the accurate mass and time tag approach to the proteome analysis of sub-cellular fractions obtained from Rhodobacter sphaeroides 2.4.1. Aerobic and photosynthetic cell cultures J Proteome Res 2006, 5(8):1940-1947. 10.1021/pr060050o 16889416
-
(2006)
J Proteome Res
, vol.5
, Issue.8
, pp. 1940-1947
-
-
Callister, S.J.1
Dominguez, M.A.2
Nicora, C.D.3
Zeng, X.4
Tavano, C.L.5
Kaplan, S.6
Donohue, T.J.7
Smith, R.D.8
Lipton, M.S.9
-
20
-
-
4444346217
-
Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis
-
10.1021/ac049208j 15373428
-
Wu CC MacCoss MJ Howell KE Matthews DE Yates JR 3rd Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis Anal Chem 2004, 76(17):4951-4959. 10.1021/ac049208j 15373428
-
(2004)
Anal Chem
, vol.76
, Issue.17
, pp. 4951-4959
-
-
Wu, C.C.1
MacCoss, M.J.2
Howell, K.E.3
Matthews, D.E.4
Yates III, J.R.5
-
21
-
-
84874657421
-
-
http://www-stat.stanford.edu/~tibs/SAM/ http://www-stat.stanford.edu/ ~tibs/SAM/
-
http://www-stat.stanford.edu/~tibs/SAM/ http://www-stat.stanford.edu/ ~tibs/SAM/ http://www-stat.stanford.edu/~tibs/SAM/
-
-
-
-
22
-
-
34548583308
-
Sulfite reduction in mycobacteria
-
2045171 17644602 10.1128/JB.00487-07
-
Pinto R Harrison JS Hsu T Jacobs WR Jr. Leyh TS Sulfite reduction in mycobacteria J Bacteriol 2007, 189(18):6714-6722. 2045171 17644602 10.1128/JB.00487-07
-
(2007)
J Bacteriol
, vol.189
, Issue.18
, pp. 6714-6722
-
-
Pinto, R.1
Harrison, J.S.2
Hsu, T.3
Jacobs Jr., W.R.4
Leyh, T.S.5
-
23
-
-
0036299641
-
Microarray analysis of the Mycobacterium tuberculosis transcriptional response to the acidic conditions found in phagosomes
-
135184 12081975 10.1128/JB.184.14.4025-4032.2002
-
Fisher MA Plikaytis BB Shinnick TM Microarray analysis of the Mycobacterium tuberculosis transcriptional response to the acidic conditions found in phagosomes J Bacteriol 2002, 184(14):4025-4032. 135184 12081975 10.1128/JB.184.14.4025-4032.2002
-
(2002)
J Bacteriol
, vol.184
, Issue.14
, pp. 4025-4032
-
-
Fisher, M.A.1
Plikaytis, B.B.2
Shinnick, T.M.3
-
24
-
-
32444442149
-
Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH
-
1367224 16452448 10.1128/JB.188.4.1633-1642.2006
-
Leaphart AB Thompson DK Huang K Alm E Wan XF Arkin A Brown SD Wu L Yan T Liu X Wickham GS Zhou J Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH J Bacteriol 2006, 188(4):1633-1642. 1367224 16452448 10.1128/JB.188.4.1633-1642.2006
-
(2006)
J Bacteriol
, vol.188
, Issue.4
, pp. 1633-1642
-
-
Leaphart, A.B.1
Thompson, D.K.2
Huang, K.3
Alm, E.4
Wan, X.F.5
Arkin, A.6
Brown, S.D.7
Wu, L.8
Yan, T.9
Liu, X.10
Wickham, G.S.11
Zhou, J.12
-
25
-
-
85007762572
-
Identification of DNA-binding proteins changed after induction of sporulation in Bacillus cereus
-
7766022
-
Matsuno K Miyamoto T Yamaguchi K Abu Sayed M Kajiwara T Hatano S Identification of DNA-binding proteins changed after induction of sporulation in Bacillus cereus Biosci Biotechnol Biochem 1995, 59(2):231-235. 7766022
-
(1995)
Biosci Biotechnol Biochem
, vol.59
, Issue.2
, pp. 231-235
-
-
Matsuno, K.1
Miyamoto, T.2
Yamaguchi, K.3
Abu Sayed, M.4
Kajiwara, T.5
Hatano, S.6
-
26
-
-
0347622754
-
pH-dependent catabolic protein expression during anaerobic growth of Escherichia coli K-12
-
303440 14679238 10.1128/JB.186.1.192-199.2004
-
Yohannes E Barnhart DM Slonczewski JL pH-dependent catabolic protein expression during anaerobic growth of Escherichia coli K-12 J Bacteriol 2004, 186(1):192-199. 303440 14679238 10.1128/JB.186.1.192-199.2004
-
(2004)
J Bacteriol
, vol.186
, Issue.1
, pp. 192-199
-
-
Yohannes, E.1
Barnhart, D.M.2
Slonczewski, J.L.3
-
27
-
-
1842577641
-
Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria
-
10.1038/nature02384 15042094
-
Trivedi OA Arora P Sridharan V Tickoo R Mohanty D Gokhale RS Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria Nature 2004, 428(6981):441-445. 10.1038/nature02384 15042094
-
(2004)
Nature
, vol.428
, Issue.6981
, pp. 441-445
-
-
Trivedi, O.A.1
Arora, P.2
Sridharan, V.3
Tickoo, R.4
Mohanty, D.5
Gokhale, R.S.6
-
29
-
-
0346882657
-
PepN is the major aminopeptidase in Escherichia coli: Insights on substrate specificity and role during sodium-salicylate-induced stress
-
10.1099/mic.0.26518-0 14663077
-
Chandu D Nandi D PepN is the major aminopeptidase in Escherichia coli: insights on substrate specificity and role during sodium-salicylate-induced stress Microbiology 2003, 149(Pt 12):3437-3447. 10.1099/mic.0.26518-0 14663077
-
(2003)
Microbiology
, vol.149
, Issue.PART 12
, pp. 3437-3447
-
-
Chandu, D.1
Nandi, D.2
-
30
-
-
0043142536
-
Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages: Insights into the Phagosomal Environment
-
2194186 12953091 10.1084/jem.20030846
-
Schnappinger D Ehrt S Voskuil MI Liu Y Mangan JA Monahan IM Dolganov G Efron B Butcher PD Nathan C Schoolnik GK Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages: Insights into the Phagosomal Environment J Exp Med 2003, 198(5):693-704. 2194186 12953091 10.1084/jem.20030846
-
(2003)
J Exp Med
, vol.198
, Issue.5
, pp. 693-704
-
-
Schnappinger, D.1
Ehrt, S.2
Voskuil, M.I.3
Liu, Y.4
Mangan, J.A.5
Monahan, I.M.6
Dolganov, G.7
Efron, B.8
Butcher, P.D.9
Nathan, C.10
Schoolnik, G.K.11
-
31
-
-
34547642714
-
Gene expression analysis of Corynebacterium glutamicum subjected to long-term lactic acid adaptation
-
1951826 17526706 10.1128/JB.00082-07
-
Jakob K Satorhelyi P Lange C Wendisch VF Silakowski B Scherer S Neuhaus K Gene expression analysis of Corynebacterium glutamicum subjected to long-term lactic acid adaptation J Bacteriol 2007, 189(15):5582-5590. 1951826 17526706 10.1128/JB.00082-07
-
(2007)
J Bacteriol
, vol.189
, Issue.15
, pp. 5582-5590
-
-
Jakob, K.1
Satorhelyi, P.2
Lange, C.3
Wendisch, V.F.4
Silakowski, B.5
Scherer, S.6
Neuhaus, K.7
-
32
-
-
38349117099
-
Determination of global protein turnover in stressed mycobacterium cells using hybrid-linear ion trap-fourier transform mass spectrometry
-
10.1021/ac701690d 18085750
-
Rao PK Roxas BA Li Q Determination of global protein turnover in stressed mycobacterium cells using hybrid-linear ion trap-fourier transform mass spectrometry Anal Chem 2008, 80(2):396-406. 10.1021/ ac701690d 18085750
-
(2008)
Anal Chem
, vol.80
, Issue.2
, pp. 396-406
-
-
Rao, P.K.1
Roxas, B.A.2
Li, Q.3
-
33
-
-
24644519314
-
Significance analysis of time course microarray experiments
-
1201697 16141318 10.1073/pnas.0504609102
-
Storey JD Xiao W Leek JT Tompkins RG Davis RW Significance analysis of time course microarray experiments Proc Natl Acad Sci U S A 2005, 102(36):12837-12842. 1201697 16141318 10.1073/pnas.0504609102
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, Issue.36
, pp. 12837-12842
-
-
Storey, J.D.1
Xiao, W.2
Leek, J.T.3
Tompkins, R.G.4
Davis, R.W.5
-
34
-
-
30744460928
-
Electron transport in the pathway of acetate conversion to methane in the marine archaeon Methanosarcina acetivorans
-
1347274 16385060 10.1128/JB.188.2.702-710.2006
-
Li Q Li L Rejtar T Lessner DJ Karger BL Ferry JG Electron transport in the pathway of acetate conversion to methane in the marine archaeon Methanosarcina acetivorans J Bacteriol 2006, 188(2):702-710. 1347274 16385060 10.1128/JB.188.2.702-710.2006
-
(2006)
J Bacteriol
, vol.188
, Issue.2
, pp. 702-710
-
-
Li, Q.1
Li, L.2
Rejtar, T.3
Lessner, D.J.4
Karger, B.L.5
Ferry, J.G.6
-
35
-
-
33749604289
-
Proteomic analysis of individual variation in normal livers of human beings using difference gel electrophoresis
-
10.1002/pmic.200600006 16947120
-
Zhang X Guo Y Song Y Sun W Yu C Zhao X Wang H Jiang H Li Y Qian X Jiang Y He F Proteomic analysis of individual variation in normal livers of human beings using difference gel electrophoresis Proteomics 2006, 6(19):5260-5268. 10.1002/pmic.200600006 16947120
-
(2006)
Proteomics
, vol.6
, Issue.19
, pp. 5260-5268
-
-
Zhang, X.1
Guo, Y.2
Song, Y.3
Sun, W.4
Yu, C.5
Zhao, X.6
Wang, H.7
Jiang, H.8
Li, Y.9
Qian, X.10
Jiang, Y.11
He, F.12
|