-
1
-
-
0032875697
-
Quantitative analysis of complex protein mixtures using isotope-coded affnity tags
-
Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affnity tags. Nat. Biotechnol. 17(10), 994-999 (1999).
-
(1999)
Nat. Biotechnol.
, vol.17
, Issue.10
, pp. 994-999
-
-
Gygi, S.P.1
Rist, B.2
Gerber, S.A.3
Turecek, F.4
Gelb, M.H.5
Aebersold, R.6
-
2
-
-
0034789979
-
Quantitative profling of differentiation-induced microsomal proteins using isotope-coded affnity tags and mass spectrometry
-
Han DK, Eng J, Zhou H, Aebersold R. Quantitative profling of differentiation-induced microsomal proteins using isotope-coded affnity tags and mass spectrometry. Nat. Biotechnol. 19(10), 946-951 (2001).
-
(2001)
Nat. Biotechnol.
, vol.19
, Issue.10
, pp. 946-951
-
-
Han, D.K.1
Eng, J.2
Zhou, H.3
Aebersold, R.4
-
3
-
-
19944432197
-
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
-
Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3(12), 1154-1169 (2004).
-
(2004)
Mol. Cell. Proteomics
, vol.3
, Issue.12
, pp. 1154-1169
-
-
Ross, P.L.1
Huang, Y.N.2
Marchese, J.N.3
-
4
-
-
0036583926
-
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
-
Ong SE, Blagoev B, Kratchmarova I et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1(5), 376-386 (2002).
-
(2002)
Mol. Cell. Proteomics
, vol.1
, Issue.5
, pp. 376-386
-
-
Ong, S.E.1
Blagoev, B.2
Kratchmarova, I.3
-
5
-
-
35848929694
-
Analysis and validation of proteomic data generated by tandem mass spectrometry
-
Nesvizhskii AI, Vitek O, Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 4(10), 787-797 (2007).
-
(2007)
Nat. Methods
, vol.4
, Issue.10
, pp. 787-797
-
-
Nesvizhskii, A.I.1
Vitek, O.2
Aebersold, R.3
-
6
-
-
33751340274
-
Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics
-
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 131(12), 1335-1341 (2006).
-
(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
-
7
-
-
38649098761
-
Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: The comparison of two quantitative methods
-
Usaite R, Wohlschlegel J, Venable JD et al. Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: the comparison of two quantitative methods. J. Proteome Res. 7(1), 266-275 (2008).
-
(2008)
J. Proteome Res.
, vol.7
, Issue.1
, pp. 266-275
-
-
Usaite, R.1
Wohlschlegel, J.2
Venable, J.D.3
-
8
-
-
13844299232
-
Integrating gene and protein expression data: Pattern analysis and profle mining
-
Cox B, Kislinger T, Emili A. Integrating gene and protein expression data: pattern analysis and profle mining. Methods 35(3), 303-314 (2005).
-
(2005)
Methods
, vol.35
, Issue.3
, pp. 303-314
-
-
Cox, B.1
Kislinger, T.2
Emili, A.3
-
9
-
-
34848822499
-
Quantitative profle of fve murine core proteomes using label-free functional proteomics
-
Cutillas PR, Vanhaesebroeck B. Quantitative profle of fve murine core proteomes using label-free functional proteomics. Mol. Cell. Proteomics 6(9), 1560-1573 (2007).
-
(2007)
Mol. Cell. Proteomics
, vol.6
, Issue.9
, pp. 1560-1573
-
-
Cutillas, P.R.1
Vanhaesebroeck, B.2
-
10
-
-
34548459898
-
Global survey of human T leukemic cells by integrating proteomics and transcriptomics profling
-
Wu L, Hwang SI, Rezaul K et al. Global survey of human T leukemic cells by integrating proteomics and transcriptomics profling. Mol. Cell. Proteomics 6(8), 1343-1353 (2007).
-
(2007)
Mol. Cell. Proteomics
, vol.6
, Issue.8
, pp. 1343-1353
-
-
Wu, L.1
Hwang, S.I.2
Rezaul, K.3
-
11
-
-
84880037648
-
LC/MS-based quantitative proteomic analysis of paraffn-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis
-
Huang SK, Darfer MM, Nicholl MB et al. LC/MS-based quantitative proteomic analysis of paraffn-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis. PLoS ONE 4(2), e4430 (2009).
-
(2009)
PLoS ONE
, vol.4
, Issue.2
-
-
Huang, S.K.1
Darfer, M.M.2
Nicholl, M.B.3
-
12
-
-
35648996970
-
Temporal analysis of sucrose-induced phosphorylation changes in plasma membrane proteins of Arabidopsis
-
Niittylä T, Fuglsang AT, Palmgren MG, Frommer WB, Schulze WX. Temporal analysis of sucrose-induced phosphorylation changes in plasma membrane proteins of Arabidopsis. Mol. Cell. Proteomics 6(10), 1711-1726 (2007).
-
(2007)
Mol. Cell. Proteomics
, vol.6
, Issue.10
, pp. 1711-1726
-
-
Niittylä, T.1
Fuglsang, A.T.2
Palmgren, M.G.3
Frommer, W.B.4
Schulze, W.X.5
-
13
-
-
34249780833
-
Stability of plant defense proteins in the gut of insect herbivores
-
Chen H, Gonzales-Vigil E, Wilkerson CG, Howe GA. Stability of plant defense proteins in the gut of insect herbivores. Plant Physiol. 143(4), 1954-1967 (2007).
-
(2007)
Plant Physiol.
, vol.143
, Issue.4
, pp. 1954-1967
-
-
Chen, H.1
Gonzales-Vigil, E.2
Wilkerson, C.G.3
Howe, G.A.4
-
14
-
-
61449237172
-
Quantitative interaction proteomics using mass spectrometry
-
Wepf A, Glatter T, Schmidt A, Aebersold R, Gstaiger M. Quantitative interaction proteomics using mass spectrometry. Nat. Methods 6(3), 203-205 (2009).
-
(2009)
Nat. Methods
, vol.6
, Issue.3
, pp. 203-205
-
-
Wepf, A.1
Glatter, T.2
Schmidt, A.3
Aebersold, R.4
Gstaiger, M.5
-
15
-
-
39849101009
-
Proteomic analysis of active multiple sclerosis lesions reveals therapeutic targets
-
Han MH, Hwang S-I, Roy DB et al. Proteomic analysis of active multiple sclerosis lesions reveals therapeutic targets. Nature 451, 1076-1081 (2008).
-
(2008)
Nature
, vol.451
, pp. 1076-1081
-
-
Han, M.H.1
Hwang, S.-I.2
Roy, D.B.3
-
16
-
-
70649083505
-
A label-free quantitative proteomic strategy to identify E3 ubiquitin ligase substrates targeted to proteasome degradation
-
Burande CF, Heuzé ML, Lamsoul I et al. A label-free quantitative proteomic strategy to identify E3 ubiquitin ligase substrates targeted to proteasome degradation. Mol. Cell. Proteomics 8(7), 1719-1727 (2009).
-
(2009)
Mol. Cell. Proteomics
, vol.8
, Issue.7
, pp. 1719-1727
-
-
Burande, C.F.1
Heuzé, M.L.2
Lamsoul, I.3
-
17
-
-
70350462371
-
Large-scale quantitative phosphoproteomic analysis of T-cell receptor signaling: System-wide modulation of protein-protein interaction mediated by site-specifc phosphorylation
-
Mayya V, Lundgren DH, Hwang S-I, Rezaul K, Wu L, Han DK. Large-scale quantitative phosphoproteomic analysis of T-cell receptor signaling: system-wide modulation of protein-protein interaction mediated by site-specifc phosphorylation. Sci. Signal. 2(84), ra46 (2009).
-
(2009)
Sci. Signal.
, vol.2
, Issue.84
-
-
Mayya, V.1
Lundgren, D.H.2
Hwang, S.-I.3
Rezaul, K.4
Wu, L.5
Han, D.K.6
-
18
-
-
65549116865
-
Label-free quantitation: A new glycoproteomics approach
-
Rebecchi KR, Wenke JL, Go EP, Desaire H. Label-free quantitation: a new glycoproteomics approach. J. Am. Soc. Mass Spectrom. 20(6), 1048-1059 (2009).
-
(2009)
J. Am. Soc. Mass Spectrom.
, vol.20
, Issue.6
, pp. 1048-1059
-
-
Rebecchi, K.R.1
Wenke, J.L.2
Go, E.P.3
Desaire, H.4
-
19
-
-
34848862125
-
Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples
-
Levin Y, Schwarz E, Wang L, Leweke FM, Bahn S. Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples. J. Sep. Sci. 30(14), 2198-2203 (2007).
-
(2007)
J. Sep. Sci.
, vol.30
, Issue.14
, pp. 2198-2203
-
-
Levin, Y.1
Schwarz, E.2
Wang, L.3
Leweke, F.M.4
Bahn, S.5
-
20
-
-
0037106398
-
Identifcation and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry Anal
-
Bondarenko PV, Chelius D, Shaler TA. Identifcation and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry Anal. Chem. 74 (18), 4741-4749 (2002).
-
(2002)
Chem.
, vol.74
, Issue.18
, pp. 4741-4749
-
-
Bondarenko, P.V.1
Chelius, D.2
Shaler, T.A.3
-
21
-
-
3242731195
-
A model for random sampling and estimation of relative protein abundance in shotgun proteomics
-
Liu H, Sadygov RG, Yates JR 3rd. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76(14), 4193-4201 (2004).
-
(2004)
Anal. Chem.
, vol.76
, Issue.14
, pp. 4193-4201
-
-
Liu, H.1
Sadygov, R.G.2
Yates III, J.R.3
-
22
-
-
12244270638
-
Differential proteomics via probabilistic peptide identifcation scores
-
Colinge J, Chiappe D, Lagache S, Moniatte M, Bougueleret L. Differential proteomics via probabilistic peptide identifcation scores. Anal. Chem. 77(2), 596-606 (2005).
-
(2005)
Anal. Chem.
, vol.77
, Issue.2
, pp. 596-606
-
-
Colinge, J.1
Chiappe, D.2
Lagache, S.3
Moniatte, M.4
Bougueleret, L.5
-
23
-
-
33644852886
-
Optimization and use of peptide mass measurement accuracy in shotgun proteomics
-
Haas W, Faherty BK, Gerber SA et al. Optimization and use of peptide mass measurement accuracy in shotgun proteomics. Mol. Cell. Proteomics 5(7), 1326-1337 (2006).
-
(2006)
Mol. Cell. Proteomics
, vol.5
, Issue.7
, pp. 1326-1337
-
-
Haas, W.1
Faherty, B.K.2
Gerber, S.A.3
-
24
-
-
34748916981
-
Quantitative mass spectrometry in proteomics: A critical review
-
Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B. Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 389(4), 1017-1031 (2007).
-
(2007)
Anal. Bioanal. Chem.
, vol.389
, Issue.4
, pp. 1017-1031
-
-
Bantscheff, M.1
Schirle, M.2
Sweetman, G.3
Rick, J.4
Kuster, B.5
-
25
-
-
0036636552
-
A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-fight (Q-TOF) mass spectrometer for studying protein phosphorylation
-
Bateman RH, Carruthers R, Hoyes JB et al. A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-fight (Q-TOF) mass spectrometer for studying protein phosphorylation. J. Am. Soc. Mass Spectrom. 13(7), 792-803 (2002).
-
(2002)
J. Am. Soc. Mass Spectrom.
, vol.13
, Issue.7
, pp. 792-803
-
-
Bateman, R.H.1
Carruthers, R.2
Hoyes, J.B.3
-
26
-
-
20144388265
-
Quantitative proteomic analysis by accurate mass retention time pairs
-
Silva JC, Denny R, Dorschel CA et al. Quantitative proteomic analysis by accurate mass retention time pairs. Anal. Chem. 77(7), 2187-2200 (2005).
-
(2005)
Anal. Chem.
, vol.77
, Issue.7
, pp. 2187-2200
-
-
Silva, J.C.1
Denny, R.2
Dorschel, C.A.3
-
27
-
-
63049084861
-
The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS
-
Geromanos SJ, Vissers JPC, Silva JC et al. The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS. Proteomics 9(6), 1683-1695 (2009).
-
(2009)
Proteomics
, vol.9
, Issue.6
, pp. 1683-1695
-
-
Geromanos, S.J.1
Vissers, J.P.C.2
Silva, J.C.3
-
28
-
-
67650351489
-
A comparison of labeling and label-free mass spectrometry-based proteomics approaches
-
Patel VJ, Thalassinos K, Slade SE et al. A comparison of labeling and label-free mass spectrometry-based proteomics approaches. J. Proteome Res. 8(7), 3752-3759 (2009).
-
(2009)
J. Proteome Res.
, vol.8
, Issue.7
, pp. 3752-3759
-
-
Patel, V.J.1
Thalassinos, K.2
Slade, S.E.3
-
29
-
-
34247365096
-
Relative quantitation of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer
-
Venable JD, Wohlschlegel J, McClatchy DB, Park SK, Yates JR 3rd. Relative quantitation of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer. Anal. Chem. 79(8), 3056-3064 (2007).
-
(2007)
Anal. Chem.
, vol.79
, Issue.8
, pp. 3056-3064
-
-
Venable, J.D.1
Wohlschlegel, J.2
McClatchy, D.B.3
Park, S.K.4
Yates III, J.R.5
-
30
-
-
38649095599
-
An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data
-
Mueller LN, Brusniak MY, Mani DR, Aebersold R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J. Proteome Res. 7(1), 51-61 (2008).
-
(2008)
J. Proteome Res.
, vol.7
, Issue.1
, pp. 51-61
-
-
Mueller, L.N.1
Brusniak, M.Y.2
Mani, D.R.3
Aebersold, R.4
-
31
-
-
26444506068
-
Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling
-
Zybailov B, Coleman MK, Florens L, Washburn MP. Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal. Chem. 77(19), 6218-6224 (2005).
-
(2005)
Anal. Chem.
, vol.77
, Issue.19
, pp. 6218-6224
-
-
Zybailov, B.1
Coleman, M.K.2
Florens, L.3
Washburn, M.P.4
-
32
-
-
41549117597
-
A quantitative analysis software tool for mass spectrometry-based proteomics
-
Park SK, Venable JD, Xu T, Yates JR 3rd. A quantitative analysis software tool for mass spectrometry-based proteomics. Nat. Methods 5(4), 319-322 (2008).
-
(2008)
Nat. Methods
, vol.5
, Issue.4
, pp. 319-322
-
-
Park, S.K.1
Venable, J.D.2
Xu, T.3
Yates III, J.R.4
-
33
-
-
67349208911
-
Bioinformatics analysis of mass spectrometry-based proteomics datasets
-
Kumar C, Mann M. Bioinformatics analysis of mass spectrometry-based proteomics datasets. FEBS Lett. 583(11), 1703-1712 (2009).
-
(2009)
FEBS Lett.
, vol.583
, Issue.11
, pp. 1703-1712
-
-
Kumar, C.1
Mann, M.2
-
34
-
-
40549107755
-
Comparative LC-MS: A landscape of peaks and valleys
-
America AH, Cordewener JH. Comparative LC-MS: a landscape of peaks and valleys. Proteomics 8(4), 731-749 (2008).
-
(2008)
Proteomics
, vol.8
, Issue.4
, pp. 731-749
-
-
America, A.H.1
Cordewener, J.H.2
-
35
-
-
27644543078
-
Comparison of label-free methods for quantifying human proteins by shotgun proteomics
-
Old WM, Meyer-Arendt K, Aveline-Wolf L et al. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 4(10), 1487-1502 (2005).
-
(2005)
Mol. Cell. Proteomics
, vol.4
, Issue.10
, pp. 1487-1502
-
-
Old, W.M.1
Meyer-Arendt, K.2
Aveline-Wolf, L.3
-
36
-
-
0142215475
-
Global analysis of protein expression in yeast
-
Ghaemmaghami S, Huh WK, Bower K et al. Global analysis of protein expression in yeast. Nature 425(6959), 737-741 (2003).
-
(2003)
Nature
, vol.425
, Issue.6959
, pp. 737-741
-
-
Ghaemmaghami, S.1
Huh, W.K.2
Bower, K.3
-
37
-
-
33745608428
-
Systematic characterization of nuclear proteome during apoptosis
-
Hwang SI, Lundgren DH, Mayya V et al. Systematic characterization of nuclear proteome during apoptosis. Mol. Cell. Proteomics 5(6),1131-1145 (2006).
-
(2006)
Mol. Cell. Proteomics
, vol.5
, Issue.6
, pp. 1131-1145
-
-
Hwang, S.I.1
Lundgren, D.H.2
Mayya, V.3
-
38
-
-
34547232157
-
Optimization of mass spectrometry-compatible surfactants for shotgun proteomics
-
Chen EI, Cociorva D, Norris JL, Yates JR 3rd. Optimization of mass spectrometry-compatible surfactants for shotgun proteomics. J. Proteome Res. 6(7), 2529-2538 (2007).
-
(2007)
J. Proteome Res.
, vol.6
, Issue.7
, pp. 2529-2538
-
-
Chen, E.I.1
Cociorva, D.2
Norris, J.L.3
Yates III, J.R.4
-
39
-
-
63649096604
-
Relationship between sample loading amount and peptide identifcation and its effects on quantitative proteomics
-
Liu K, Zhang J, Wang J. Relationship between sample loading amount and peptide identifcation and its effects on quantitative proteomics. Anal. Chem. 81(4), 1307-1314 (2009).
-
(2009)
Anal. Chem.
, vol.81
, Issue.4
, pp. 1307-1314
-
-
Liu, K.1
Zhang, J.2
Wang, J.3
-
40
-
-
33846165487
-
Absolute protein expression profling estimates the relative contributions of transcriptional and translational regulation
-
Lu P, Vogel C, Wang R, Yao X, Marcotte EM. Absolute protein expression profling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 25(1), 117-124 (2007).
-
(2007)
Nat. Biotechnol.
, vol.25
, Issue.1
, pp. 117-124
-
-
Lu, P.1
Vogel, C.2
Wang, R.3
Yao, X.4
Marcotte, E.M.5
-
41
-
-
33846133955
-
Computational prediction of proteotypic peptides for quantitative proteomics
-
Mallick P, Schirle M, Chen SS et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 25(1), 125-131 (2007).
-
(2007)
Nat. Biotechnol.
, vol.25
, Issue.1
, pp. 125-131
-
-
Mallick, P.1
Schirle, M.2
Chen, S.S.3
-
42
-
-
34848854494
-
Peptide correlation: A means to identify high quality quantitative information in large-scale proteomic studies
-
Schwarz E, Levin Y, Wang L, Leweke FM, Bahn S. Peptide correlation: a means to identify high quality quantitative information in large-scale proteomic studies. J. Sep. Sci. 30(14), 2190-2197 (2007).
-
(2007)
J. Sep. Sci.
, vol.30
, Issue.14
, pp. 2190-2197
-
-
Schwarz, E.1
Levin, Y.2
Wang, L.3
Leweke, F.M.4
Bahn, S.5
-
43
-
-
68049085754
-
Effect of dynamic exclusion duration on spectral count based quantitative proteomics
-
Zhang Y, Wen Z, Washburn MP, Florens L. Effect of dynamic exclusion duration on spectral count based quantitative proteomics. Anal. Chem. 81(15), 6317-6326 (2009).
-
(2009)
Anal. Chem.
, vol.81
, Issue.15
, pp. 6317-6326
-
-
Zhang, Y.1
Wen, Z.2
Washburn, M.P.3
Florens, L.4
-
44
-
-
38649129756
-
The effects of shared peptides on protein quantitation in label-free proteomics by LC/MS/MS
-
Jin S, Daly DS, Springer DL, Miller JH. The effects of shared peptides on protein quantitation in label-free proteomics by LC/MS/MS. J. Proteome Res. 7(1), 164-169 (2008).
-
(2008)
J. Proteome Res.
, vol.7
, Issue.1
, pp. 164-169
-
-
Jin, S.1
Daly, D.S.2
Springer, D.L.3
Miller, J.H.4
-
45
-
-
33748319353
-
Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae
-
Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP. Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J. Proteome Res. 5(9), 2339-2347 (2006).
-
(2006)
J. Proteome Res.
, vol.5
, Issue.9
, pp. 2339-2347
-
-
Zybailov, B.1
Mosley, A.L.2
Sardiu, M.E.3
Coleman, M.K.4
Florens, L.5
Washburn, M.P.6
-
46
-
-
44449161040
-
Mixed-effects statistical model for comparative LC-MS proteomics studies
-
Daly DS, Anderson KK, Panisko EA et al. Mixed-effects statistical model for comparative LC-MS proteomics studies. J. Proteome Res. 7(3), 1209-1217 (2008).
-
(2008)
J. Proteome Res.
, vol.7
, Issue.3
, pp. 1209-1217
-
-
Daly, D.S.1
Anderson, K.K.2
Panisko, E.A.3
-
47
-
-
60649101258
-
The APEX quantitative proteomics tool: Generating protein quantitation estimates from LC-MS/MS proteomics results
-
Braisted JC, Kuntumalla S, Vogel C et al. The APEX quantitative proteomics tool: generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics 9, 529-539 (2008).
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 529-539
-
-
Braisted, J.C.1
Kuntumalla, S.2
Vogel, C.3
-
48
-
-
0042338362
-
A statistical model for identifying proteins by tandem mass spectrometry
-
Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75(17), 4646-4658 (2003).
-
(2003)
Anal. Chem.
, vol.75
, Issue.17
, pp. 4646-4658
-
-
Nesvizhskii, A.I.1
Keller, A.2
Kolker, E.3
Aebersold, R.4
-
49
-
-
0033434080
-
Probability-based protein identifcation by searching sequence databases using mass spectrometry data
-
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identifcation by searching sequence databases using mass spectrometry data. Electrophoresis 20 (18), 3551-3567 (1999).
-
(1999)
Electrophoresis
, vol.20
, Issue.18
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.2
Creasy, D.M.3
Cottrell, J.S.4
-
50
-
-
39049122146
-
Proteomics analysis of serum from mutant mice reveals lysosomal proteins selectively transported by each of the two mannose 6-phosphate receptors
-
Qian M, Sleat DE, Zheng H, Moore D, Lobel P. Proteomics analysis of serum from mutant mice reveals lysosomal proteins selectively transported by each of the two mannose 6-phosphate receptors. Mol. Cell. Proteomics 7(1), 58-70 (2008).
-
(2008)
Mol. Cell. Proteomics
, vol.7
, Issue.1
, pp. 58-70
-
-
Qian, M.1
Sleat, D.E.2
Zheng, H.3
Moore, D.4
Lobel, P.5
-
52
-
-
42649131100
-
Statistical similarities between transcriptomics and quantitative shotgun proteomics data
-
Pavelka N, Fournier ML, Swanson SK et al. Statistical similarities between transcriptomics and quantitative shotgun proteomics data. Mol. Cell. Proteomics 7(4), 631-644 (2008).
-
(2008)
Mol. Cell. Proteomics
, vol.7
, Issue.4
, pp. 631-644
-
-
Pavelka, N.1
Fournier, M.L.2
Swanson, S.K.3
-
53
-
-
58149299336
-
Signifcance analysis of spectral count data in label-free shotgun proteomics
-
Choi H, Fermin D, Nesvizhskii AI. Signifcance analysis of spectral count data in label-free shotgun proteomics. Mol. Cell. Proteomics 7(12), 2373-2385 (2008).
-
(2008)
Mol. Cell. Proteomics
, vol.7
, Issue.12
, pp. 2373-2385
-
-
Choi, H.1
Fermin, D.2
Nesvizhskii, A.I.3
-
54
-
-
0036674269
-
Large-scale proteomic analysis of the human spliceosome
-
DOI 10.1101/gr.473902
-
Rappsilber J, Ryder U, Lamond AI, Mann M. Large-scale proteomic analysis of the human spliceosome. Genome Res. 12(8), 1231-1245 (2002). (Pubitemid 41264425)
-
(2002)
Genome Research
, vol.12
, Issue.8
, pp. 1231-1245
-
-
Rappsilber, J.1
Ryder, U.2
Lamond, A.I.3
Mann, M.4
-
55
-
-
26844559000
-
Exponentially modifed protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
-
Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M. Exponentially modifed protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 4(9), 1265-1272 (2005).
-
(2005)
Mol. Cell. Proteomics
, vol.4
, Issue.9
, pp. 1265-1272
-
-
Ishihama, Y.1
Oda, Y.2
Tabata, T.3
Sato, T.4
Nagasu, T.5
Rappsilber, J.6
Mann, M.7
-
56
-
-
3543005925
-
Cluster analysis of mass spectrometry data reveals a novel component of SAGA
-
Powell DW, Weaver CM, Jennings JL et al. Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Mol. Cell. Biol. 24(16), 7249-7259 (2004).
-
(2004)
Mol. Cell. Biol.
, vol.24
, Issue.16
, pp. 7249-7259
-
-
Powell, D.W.1
Weaver, C.M.2
Jennings, J.L.3
-
57
-
-
2442683994
-
Semiquantitative proteomic analysis of rat forebrain postsynaptic density fractions by mass spectrometry J
-
Peng J, Kim MJ, Cheng D, Duong DM, Gygi SP, Sheng M. Semiquantitative proteomic analysis of rat forebrain postsynaptic density fractions by mass spectrometry J. Biol. Chem. 279(20), 21003-21011 (2004).
-
(2004)
Biol. Chem.
, vol.279
, Issue.20
, pp. 21003-21011
-
-
Peng, J.1
Kim, M.J.2
Cheng, D.3
Duong, D.M.4
Gygi, S.P.5
Sheng, M.6
-
58
-
-
41149127192
-
A label-free quantitation method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen
-
Asara JM, Christofk HR, Freimark LM, Cantley LC. A label-free quantitation method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen. Proteomics 8(5), 994-999 (2008).
-
(2008)
Proteomics
, vol.8
, Issue.5
, pp. 994-999
-
-
Asara, J.M.1
Christofk, H.R.2
Freimark, L.M.3
Cantley, L.C.4
-
59
-
-
0036269973
-
Proteomics of the eukaryotic transcription machinery: Identifcation of proteins associated with components of yeast TFIID by multidimensional mass spectrometry
-
Sanders SL, Jennings J, Canutescu A, Link AJ, Weil PA. Proteomics of the eukaryotic transcription machinery: identifcation of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol. Cell. Biol. 22(13), 4723-4738 (2002).
-
(2002)
Mol. Cell. Biol.
, vol.22
, Issue.13
, pp. 4723-4738
-
-
Sanders, S.L.1
Jennings, J.2
Canutescu, A.3
Link, A.J.4
Weil, P.A.5
-
60
-
-
63649131272
-
Validation of gel-free, label-free quantitative proteomics approaches: Applications for seed allergen profling
-
Stevenson SE, Chu Y, Ozias-Akins P, Thelen JJ. Validation of gel-free, label-free quantitative proteomics approaches: applications for seed allergen profling. J. Proteomics 72(3), 555-566 (2009).
-
(2009)
J. Proteomics
, vol.72
, Issue.3
, pp. 555-566
-
-
Stevenson, S.E.1
Chu, Y.2
Ozias-Akins, P.3
Thelen, J.J.4
-
61
-
-
41549150673
-
Comparative proteomics profling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses
-
Gramolini AO, Kislinger T, Alikhani-Koopaei R et al. Comparative proteomics profling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses. Mol. Cell. Proteomics 7(3), 519-533 (2008).
-
(2008)
Mol. Cell. Proteomics
, vol.7
, Issue.3
, pp. 519-533
-
-
Gramolini, A.O.1
Kislinger, T.2
Alikhani-Koopaei, R.3
-
62
-
-
3543075240
-
In vitro and in silico processes to identify differentially expressed proteins
-
Allet N, Barrillat N, Baussant T et al In vitro and in silico processes to identify differentially expressed proteins. Proteomics 4(8), 2333-2351 (2004).
-
(2004)
Proteomics
, vol.4
, Issue.8
, pp. 2333-2351
-
-
Allet, N.1
Barrillat, N.2
Baussant, T.3
-
63
-
-
44449086044
-
Spectral index for assessment of differential protein expression in shotgun proteomics
-
Fu X, Gharib SA, Green PS et al. Spectral index for assessment of differential protein expression in shotgun proteomics. J. Proteome Res. 7(3), 845-854 (2008).
-
(2008)
J. Proteome Res.
, vol.7
, Issue.3
, pp. 845-854
-
-
Fu, X.1
Gharib, S.A.2
Green, P.S.3
-
64
-
-
0037015602
-
A proteomic view of the Plasmodium falciparum life cycle
-
Florens L, Washburn MP, Raine JD et al. A proteomic view of the Plasmodium falciparum life cycle. Nature 419(6906), 520-526 (2002).
-
(2002)
Nature
, vol.419
, Issue.6906
, pp. 520-526
-
-
Florens, L.1
Washburn, M.P.2
Raine, J.D.3
-
65
-
-
58149295188
-
Label-free quantitative analysis of one-dimensional PAGE LC/MS/MS proteome
-
Gao B-B, Stuart L, Feener EP. Label-free quantitative analysis of one-dimensional PAGE LC/MS/MS proteome. Mol. Cell. Proteomics 7(12), 2399-2409 (2008).
-
(2008)
Mol. Cell. Proteomics
, vol.7
, Issue.12
, pp. 2399-2409
-
-
Gao, B.-B.1
Stuart, L.2
Feener, E.P.3
-
66
-
-
33750987637
-
Detecting differential and correlated protein expression in label-free shotgun proteomics
-
Zhang B, VerBerkmoes NC, Langston MA, Uberbacher E, Hettich RL, Samatova NF. Detecting differential and correlated protein expression in label-free shotgun proteomics. J. Proteome Res. 5(11), 2909-2918 (2006).
-
(2006)
J. Proteome Res.
, vol.5
, Issue.11
, pp. 2909-2918
-
-
Zhang, B.1
Verberkmoes, N.C.2
Langston, M.A.3
Uberbacher, E.4
Hettich, R.L.5
Samatova, N.F.6
-
67
-
-
33645993265
-
Global survey of organ and organelle protein expression in mouse: Combined proteomic and transcriptomic profling
-
Kislinger T, Cox B, Kannan A et al. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profling. Cell 125(1), 173-186 (2006).
-
(2006)
Cell
, vol.125
, Issue.1
, pp. 173-186
-
-
Kislinger, T.1
Cox, B.2
Kannan, A.3
-
68
-
-
33845500104
-
Quantitative proteomics analysis of the secretory pathway
-
Gilchrist A, Au CE, Hiding J et al. Quantitative proteomics analysis of the secretory pathway. Cell 127(6), 1265-1281 (2006).
-
(2006)
Cell
, vol.127
, Issue.6
, pp. 1265-1281
-
-
Gilchrist, A.1
Au, C.E.2
Hiding, J.3
-
69
-
-
34548428842
-
ABRF-PRG2006 study: Relative protein quantitation
-
Turck CW, Falick AM, Kowalak JA et al. ABRF-PRG2006 study: relative protein quantitation. Mol. Cell. Proteomics 6(8), 1291-1298 (2007).
-
(2007)
Mol. Cell. Proteomics
, vol.6
, Issue.8
, pp. 1291-1298
-
-
Turck, C.W.1
Falick, A.M.2
Kowalak, J.A.3
-
70
-
-
0037795741
-
Absolute quantitation of proteins and phosphoproteins from cell lysates by tandem MS
-
Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantitation of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl Acad. Sci. USA 100(12), 6940-6945 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, Issue.12
, pp. 6940-6945
-
-
Gerber, S.A.1
Rush, J.2
Stemman, O.3
Kirschner, M.W.4
Gygi, S.P.5
-
71
-
-
61449237172
-
Quantitative interaction proteomics using mass spectrometry
-
Wepf A, Glatter T, Schmidt A, Aebersold R, Gstaiger M. Quantitative interaction proteomics using mass spectrometry. Nat. Methods 6(3), 203-205 (2009).
-
(2009)
Nat. Methods
, vol.6
, Issue.3
, pp. 203-205
-
-
Wepf, A.1
Glatter, T.2
Schmidt, A.3
Aebersold, R.4
Gstaiger, M.5
-
72
-
-
23144442824
-
Multiplexed absolute quantitation in proteomics using artifcial QCAT proteins of concatenated signature peptides
-
Beynon RJ, Doherty MK, Pratt JM, Gaskell SJ. Multiplexed absolute quantitation in proteomics using artifcial QCAT proteins of concatenated signature peptides. Nat. Methods 2(8), 587-589 (2005).
-
(2005)
Nat. Methods
, vol.2
, Issue.8
, pp. 587-589
-
-
Beynon, R.J.1
Doherty, M.K.2
Pratt, J.M.3
Gaskell, S.J.4
-
73
-
-
38349037650
-
Isotope-labeled protein standards: Toward absolute quantitative proteomics
-
Brun V, Dupuis A, Adrait A et al. Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol. Cell. Proteomics 6(12), 2139-2149 (2007).
-
(2007)
Mol. Cell. Proteomics
, vol.6
, Issue.12
, pp. 2139-2149
-
-
Brun, V.1
Dupuis, A.2
Adrait, A.3
-
74
-
-
0142179210
-
Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays
-
Jain N, Thatte J, Braciale T, Ley K, O'Connell M, Lee JK. Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays. Bioinformatics 19(15), 1945-1951 (2003).
-
(2003)
Bioinformatics
, vol.19
, Issue.15
, pp. 1945-1951
-
-
Jain, N.1
Thatte, J.2
Braciale, T.3
Ley, K.4
O'Connell, M.5
Lee, J.K.6
-
76
-
-
0004249246
-
-
(3rd Edition). WH Freeman and Company NY, USA
-
Sokal RR, Rohlf FJ. Biometry (3rd Edition). WH Freeman and Company, NY, USA (1995).
-
(1995)
Biometry
-
-
Sokal, R.R.1
Rohlf, F.J.2
-
77
-
-
0030681260
-
The signifcance of digital gene expression profles
-
Audic S, Claverie JM. The signifcance of digital gene expression profles. Genome Res. 7(10), 986-995 (1997).
-
(1997)
Genome Res.
, vol.7
, Issue.10
, pp. 986-995
-
-
Audic, S.1
Claverie, J.M.2
-
78
-
-
48249119082
-
PatternLab for proteomics: A tool for differential shotgun proteomics
-
Carvalho PC, Fischer JS, Chen EI, Yates JR 3rd, Barbosa VC. PatternLab for proteomics: a tool for differential shotgun proteomics. BMC Bioinformatics 9, 316-329 (2008).
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 316-329
-
-
Carvalho, P.C.1
Fischer, J.S.2
Chen, E.I.3
Yates III, J.R.4
Barbosa, V.C.5
-
79
-
-
13244292335
-
A power law global error model for the identifcation of differentially expressed genes in microarray data
-
Pavelka N, Pelizzola M, Vizzardelli C et al. A power law global error model for the identifcation of differentially expressed genes in microarray data. BMC Bioinformatics 5, 203-214 (2004).
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 203-214
-
-
Pavelka, N.1
Pelizzola, M.2
Vizzardelli, C.3
-
81
-
-
2142732441
-
Large-scale simultaneous hypothesis testing: The choice of a null hypothesis
-
Efron B. Large-scale simultaneous hypothesis testing: the choice of a null hypothesis. J. Amer. Stat. Assoc. 99(465), 96-104 (2004).
-
(2004)
J. Amer. Stat. Assoc.
, vol.99
, Issue.465
, pp. 96-104
-
-
Efron, B.1
-
82
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B 57(1), 289-300 (1995).
-
(1995)
J. R. Statist. Soc. B
, vol.57
, Issue.1
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
83
-
-
0035942271
-
Signifcance analysis of microarrays applied to the ionizing radiation response
-
Tusher VG, Tibshirani R, Chu G. Signifcance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98(9), 5116-5121 (2001).
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, Issue.9
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
84
-
-
0042424602
-
Statistical signifcance for genomewide studies
-
Storey JD, Tibshirani R. Statistical signifcance for genomewide studies. Proc. Natl Acad. Sci. USA 100(16), 9440-9445 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, Issue.16
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
-
85
-
-
19344366781
-
A practical false discovery rate approach to identifying patterns of differential expression in microarray data
-
Grant GR, Liu J, Stoeckert CJ Jr. A practical false discovery rate approach to identifying patterns of differential expression in microarray data. Bioinformatics 21(11), 2684-2690 (2005).
-
(2005)
Bioinformatics
, vol.21
, Issue.11
, pp. 2684-2690
-
-
Grant, G.R.1
Liu, J.2
Stoeckert Jr., C.J.3
-
86
-
-
28444438861
-
A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data
-
Xie Y, Pan W, Khodursky AB. A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data. Bioinformatics 21(23), 4280-4288 (2005).
-
(2005)
Bioinformatics
, vol.21
, Issue.23
, pp. 4280-4288
-
-
Xie, Y.1
Pan, W.2
Khodursky, A.B.3
-
87
-
-
38649126540
-
What's driving false discovery rates? J
-
Tabb DL. What's driving false discovery rates? J. Proteome Res. 7(1), 45-46 (2008).
-
(2008)
Proteome Res.
, vol.7
, Issue.1
, pp. 45-46
-
-
Tabb, D.L.1
-
88
-
-
38649083118
-
Assigning signifcance to peptides identifed by tandem mass spectrometry using decoy databases
-
Käll L, Storey JD, MacCoss MJ, Noble WS. Assigning signifcance to peptides identifed by tandem mass spectrometry using decoy databases. J. Proteome Res. 7(1), 29-34 (2008).
-
(2008)
J. Proteome Res.
, vol.7
, Issue.1
, pp. 29-34
-
-
Käll, L.1
Storey, J.D.2
MacCoss, M.J.3
Noble, W.S.4
-
89
-
-
38649129079
-
Posterior error probabilities and false discovery rates: Two sides of the same coin
-
Käll L, Storey JD, MacCoss MJ, Noble WS. Posterior error probabilities and false discovery rates: two sides of the same coin. J. Proteome Res. 7(1), 40-44 (2008).
-
(2008)
J. Proteome Res.
, vol.7
, Issue.1
, pp. 40-44
-
-
Käll, L.1
Storey, J.D.2
MacCoss, M.J.3
Noble, W.S.4
-
90
-
-
38349166945
-
A hierarchical statistical model to assess the confdence of peptides and proteins inferred from tandem mass spectrometry
-
Shen C, Wang Z, Shankar G, Zhang X, Li L. A hierarchical statistical model to assess the confdence of peptides and proteins inferred from tandem mass spectrometry. Bioinformatics 24(2), 202-208 (2008).
-
(2008)
Bioinformatics
, vol.24
, Issue.2
, pp. 202-208
-
-
Shen, C.1
Wang, Z.2
Shankar, G.3
Zhang, X.4
Li, L.5
-
91
-
-
63049091003
-
Bayesian nonparametric model for the validation of peptide identifcation in shotgun proteomics
-
Zhang J, Ma J, Dou L et al. Bayesian nonparametric model for the validation of peptide identifcation in shotgun proteomics. Mol. Cell. Proteomics 8(3), 547-557 (2009).
-
(2009)
Mol. Cell. Proteomics
, vol.8
, Issue.3
, pp. 547-557
-
-
Zhang, J.1
Ma, J.2
Dou, L.3
-
92
-
-
66749171697
-
Statistical design of quantitative mass spectrometry-based proteomic experiments
-
Oberg AL, Vitek O. Statistical design of quantitative mass spectrometry-based proteomic experiments. J. Proteome Res. 8(5), 2144-2156 (2009).
-
(2009)
J. Proteome Res.
, vol.8
, Issue.5
, pp. 2144-2156
-
-
Oberg, A.L.1
Vitek, O.2
|