-
1
-
-
84862683358
-
Obesidomics: Contribution of adipose tissue secretome analysis to obesity research
-
Pardo M, Roca-Rivada A, Seoane LM, Casanueva FF 2012 Obesidomics: contribution of adipose tissue secretome analysis to obesity research. Endocrine 41:374-383
-
(2012)
Endocrine
, vol.41
, pp. 374-383
-
-
Pardo, M.1
Roca-Rivada, A.2
Seoane, L.M.3
Casanueva, F.F.4
-
2
-
-
58149194632
-
Petabytescale innovations at the European Nucleotide Archive
-
Cochrane G, Akhtar R, Bonfield J, Bower L, Demiralp F, Faruque N, Gibson R, Hoad G, Hubbard T, Hunter C, Jang M, Juhos S, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Plaister S, Radhakrishnan R, Robinson S, Sobhany S, Hoopen PT, Vaughan R, Zalunin V, Birney E 2009 Petabytescale innovations at the European Nucleotide Archive. Nucleic Acids Res 37:D19-D25
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Cochrane, G.1
Akhtar, R.2
Bonfield, J.3
Bower, L.4
Demiralp, F.5
Faruque, N.6
Gibson, R.7
Hoad, G.8
Hubbard, T.9
Hunter, C.10
Jang, M.11
Juhos, S.12
Leinonen, R.13
Leonard, S.14
Lin, Q.15
Lopez, R.16
Lorenc, D.17
McWilliam, H.18
Mukherjee, G.19
Plaister, S.20
Radhakrishnan, R.21
Robinson, S.22
Sobhany, S.23
Hoopen, P.T.24
Vaughan, R.25
Zalunin, V.26
Birney, E.27
more..
-
4
-
-
57049093397
-
Much room for improvement in deposition rates of expression microarray datasets
-
Ochsner SA, Steffen DL, Stoeckert Jr CJ, McKenna NJ 2008 Much room for improvement in deposition rates of expression microarray datasets. Nat Methods 5:991
-
(2008)
Nat Methods
, vol.5
, pp. 991
-
-
Ochsner, S.A.1
Steffen, D.L.2
Stoeckert, C.J.3
McKenna, N.J.4
-
5
-
-
33847246805
-
Oncomine 3.0: Genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles
-
Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM 2007 Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 9:166-180
-
(2007)
Neoplasia
, vol.9
, pp. 166-180
-
-
Rhodes, D.R.1
Kalyana-Sundaram, S.2
Mahavisno, V.3
Varambally, R.4
Yu, J.5
Briggs, B.B.6
Barrette, T.R.7
Anstet, M.J.8
Kincead-Beal, C.9
Kulkarni, P.10
Varambally, S.11
Ghosh, D.12
Chinnaiyan, A.M.13
-
6
-
-
84865808915
-
Transcriptomine, a web resource for mining nuclear receptor signaling transcriptomes
-
10.1152/physiolgenomics.00033
-
Ochsner SA, Watkins C, McOwiti A, Dehart M, Darlington Y, Xu X, Cooney AJ, Steffen D, Becnel LB, McKenna NJ 2012 Transcriptomine, a web resource for mining nuclear receptor signaling transcriptomes. Physiol Genomics 10.1152/physiolgenomics.00033
-
(2012)
Physiol Genomics
, pp. 00033
-
-
Ochsner, S.A.1
Watkins, C.2
McOwiti, A.3
Dehart, M.4
Darlington, Y.5
Xu, X.6
Cooney, A.J.7
Steffen, D.8
Becnel, L.B.9
McKenna, N.J.10
-
7
-
-
0031398974
-
Protein identification in the post-genome era: The rapid rise of proteomics
-
James P 1997 Protein identification in the post-genome era: the rapid rise of proteomics. Q Rev Biophys 30:279-331
-
(1997)
Q Rev Biophys
, vol.30
, pp. 279-331
-
-
James, P.1
-
9
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray
-
Schena M, Shalon D, Davis RW, Brown PO 1995 Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
10
-
-
0035887145
-
ChinnaiyanAM2001 Profiling of cancer cells using protein microarrays: Discovery of novel radiation-regulated proteins
-
Sreekumar A, Nyati MK, Varambally S, Barrette TR, Ghosh D, Lawrence TS, ChinnaiyanAM2001 Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. Cancer Res 61:7585-7593
-
Cancer Res
, vol.61
, pp. 7585-7593
-
-
Sreekumar, A.1
Nyati, M.K.2
Varambally, S.3
Barrette, T.R.4
Ghosh, D.5
Lawrence, T.S.6
-
11
-
-
0035221240
-
Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions
-
RESEARCH0004
-
Haab BB, Dunham MJ, Brown PO 2001 Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol 2:RESEARCH0004
-
(2001)
Genome Biol
, vol.2
-
-
Haab, B.B.1
Dunham, M.J.2
Brown, P.O.3
-
12
-
-
0034948029
-
Array-based ELISAs for high-throughput analysis of human cytokines
-
Moody MD, Van Arsdell SW, Murphy KP, Orencole SF, Burns C 2001 Array-based ELISAs for high-throughput analysis of human cytokines. Biotechniques 31:186-190, 192-194
-
(2001)
Biotechniques
, vol.31
-
-
Moody, M.D.1
van Arsdell, S.W.2
Murphy, K.P.3
Orencole, S.F.4
Burns, C.5
-
13
-
-
0032881726
-
High-throughput microarray-based enzymelinked immunosorbent assay (ELISA)
-
Mendoza LG, McQuary P, Mongan A, Gangadharan R, Brignac S, Eggers M 1999 High-throughput microarray-based enzymelinked immunosorbent assay (ELISA). Biotechniques 27:778-780, 782-786, 788
-
(1999)
Biotechniques
, vol.27
-
-
Mendoza, L.G.1
McQuary, P.2
Mongan, A.3
Gangadharan, R.4
Brignac, S.5
Eggers, M.6
-
14
-
-
0005620475
-
Aptamers as therapeutic and diagnostic agents
-
Brody EN, Gold L 2000 Aptamers as therapeutic and diagnostic agents. J Biotechnol 74:5-13
-
(2000)
J Biotechnol
, vol.74
, pp. 5-13
-
-
Brody, E.N.1
Gold, L.2
-
15
-
-
0034936573
-
In vitro selection of nucleoprotein enzymes
-
Robertson MP, Ellington AD 2001 In vitro selection of nucleoprotein enzymes. Nat Biotechnol 19:650-655
-
(2001)
Nat Biotechnol
, vol.19
, pp. 650-655
-
-
Robertson, M.P.1
Ellington, A.D.2
-
16
-
-
80555156102
-
Surface plasmon resonance for proteomics
-
de Mol NJ 2012 Surface plasmon resonance for proteomics. Methods Mol Biol 800:33-53
-
(2012)
Methods Mol Biol
, vol.800
, pp. 33-53
-
-
de Mol, N.J.1
-
17
-
-
79959966646
-
Protein pathway activation mapping of brain metastasis from lung and breast cancers reveals organ type specific drug target activation
-
Improta G, Zupa A, Fillmore H, Deng J, Aieta M, Musto P, Liotta LA, Broaddus W, Petricoin 3rd EF, Wulfkuhle JD 2011 Protein pathway activation mapping of brain metastasis from lung and breast cancers reveals organ type specific drug target activation. J Proteome Res 10:3089-3097
-
(2011)
J Proteome Res
, vol.10
, pp. 3089-3097
-
-
Improta, G.1
Zupa, A.2
Fillmore, H.3
Deng, J.4
Aieta, M.5
Musto, P.6
Liotta, L.A.7
Broaddus, W.8
Petricoin, E.F.9
Wulfkuhle, J.D.10
-
18
-
-
80054952604
-
Profiling signalling pathways in formalin-fixed and paraffin-embedded breast cancer tissues reveals cross-talk between EGFR, HER2, HER3 and uPAR
-
Berg D, Wolff C, Malinowsky K, Tran K, Walch A, Bronger H, Schuster T, Höfler H, Becker KF 2012 Profiling signalling pathways in formalin-fixed and paraffin-embedded breast cancer tissues reveals cross-talk between EGFR, HER2, HER3 and uPAR. J Cell Physiol 227:204-212
-
(2012)
J Cell Physiol
, vol.227
, pp. 204-212
-
-
Berg, D.1
Wolff, C.2
Malinowsky, K.3
Tran, K.4
Walch, A.5
Bronger, H.6
Schuster, T.7
Höfler, H.8
Becker, K.F.9
-
19
-
-
33750456480
-
Reverse phase protein array: Validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells
-
Tibes R, Qiu Y, Lu Y, Hennessy B, Andreeff M, Mills GB, Kornblau SM 2006 Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells. Mol Cancer Ther 5:2512-2521
-
(2006)
Mol Cancer Ther
, vol.5
, pp. 2512-2521
-
-
Tibes, R.1
Qiu, Y.2
Lu, Y.3
Hennessy, B.4
Andreeff, M.5
Mills, G.B.6
Kornblau, S.M.7
-
21
-
-
0242406333
-
Utility of reverse phase protein arrays: Applications to signalling pathways and human body arrays
-
Charboneau L, Tory H, Scott H, Chen T, Winters M, Petricoin 3rd EF, Liotta LA, Paweletz CP 2002 Utility of reverse phase protein arrays: applications to signalling pathways and human body arrays. Brief Funct Genomic Proteomic 1:305-315
-
(2002)
Brief Funct Genomic Proteomic
, vol.1
, pp. 305-315
-
-
Charboneau, L.1
Tory, H.2
Scott, H.3
Chen, T.4
Winters, M.5
Petricoin, E.F.6
Liotta, L.A.7
Paweletz, C.P.8
-
22
-
-
10744226821
-
Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays
-
Nishizuka S, Charboneau L, Young L, Major S, Reinhold WC, Waltham M, Kouros-Mehr H, Bussey KJ, Lee JK, Espina V, Munson PJ, Petricoin 3rd E, Liotta LA, Weinstein JN 2003 Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc Natl Acad Sci USA 100: 14229-14234
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 14229-14234
-
-
Nishizuka, S.1
Charboneau, L.2
Young, L.3
Major, S.4
Reinhold, W.C.5
Waltham, M.6
Kouros-Mehr, H.7
Bussey, K.J.8
Lee, J.K.9
Espina, V.10
Munson, P.J.11
Petricoin, E.12
Liotta, L.A.13
Weinstein, J.N.14
-
23
-
-
5644229499
-
Regulation of gene expression by a metabolic enzyme
-
Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M 2004 Regulation of gene expression by a metabolic enzyme. Science 306:482-484
-
(2004)
Science
, vol.306
, pp. 482-484
-
-
Hall, D.A.1
Zhu, H.2
Zhu, X.3
Royce, T.4
Gerstein, M.5
Snyder, M.6
-
24
-
-
3042757210
-
Self-assembling protein microarrays
-
Ramachandran N, Hainsworth E, Bhullar B, Eisenstein S, Rosen B, Lau AY, Walter JC, LaBaer J 2004 Self-assembling protein microarrays. Science 305:86-90
-
(2004)
Science
, vol.305
, pp. 86-90
-
-
Ramachandran, N.1
Hainsworth, E.2
Bhullar, B.3
Eisenstein, S.4
Rosen, B.5
Lau, A.Y.6
Walter, J.C.7
Labaer, J.8
-
25
-
-
44449102838
-
Next-generation highdensity self-assembling functional protein arrays
-
Ramachandran N, Raphael JV, Hainsworth E, Demirkan G, Fuentes MG, Rolfs A, Hu Y, LaBaer J 2008 Next-generation highdensity self-assembling functional protein arrays. Nat Methods 5:535-538
-
(2008)
Nat Methods
, vol.5
, pp. 535-538
-
-
Ramachandran, N.1
Raphael, J.V.2
Hainsworth, E.3
Demirkan, G.4
Fuentes, M.G.5
Rolfs, A.6
Hu, Y.7
Labaer, J.8
-
26
-
-
38749109222
-
Printing protein arrays from DNA arrays
-
He M, Stoevesandt O, Palmer EA, Khan F, Ericsson O, Taussig MJ 2008 Printing protein arrays from DNA arrays. Nat Methods 5:175-177
-
(2008)
Nat Methods
, vol.5
, pp. 175-177
-
-
He, M.1
Stoevesandt, O.2
Palmer, E.A.3
Khan, F.4
Ericsson, O.5
Taussig, M.J.6
-
27
-
-
79953701026
-
Cell free expression put on the spot: Advances in repeatable protein arraying from DNA (DAPA)
-
Stoevesandt O, Vetter M, Kastelic D, Palmer EA, He M, Taussig MJ 2011 Cell free expression put on the spot: advances in repeatable protein arraying from DNA (DAPA). N Biotechnol 28:282-290
-
(2011)
N Biotechnol
, vol.28
, pp. 282-290
-
-
Stoevesandt, O.1
Vetter, M.2
Kastelic, D.3
Palmer, E.A.4
He, M.5
Taussig, M.J.6
-
28
-
-
77449146554
-
In situ biosynthesis of peptide arrays
-
He M, Stoevesandt O 2010 In situ biosynthesis of peptide arrays. Methods Mol Biol 615:345-356
-
(2010)
Methods Mol Biol
, vol.615
, pp. 345-356
-
-
He, M.1
Stoevesandt, O.2
-
29
-
-
0035430843
-
Single step generation of protein arrays fromDNAby cell-free expression and in situ immobilisation (PISA method)
-
E73-E73
-
He M, Taussig MJ 2001 Single step generation of protein arrays fromDNAby cell-free expression and in situ immobilisation (PISA method). Nucleic Acids Res 29:E73-E73
-
(2001)
Nucleic Acids Res
, vol.29
-
-
He, M.1
Taussig, M.J.2
-
30
-
-
79958278798
-
Protein-protein interactions: An application of Tus-Ter mediated protein microarray system
-
Sitaraman K, Chatterjee DK 2011 Protein-protein interactions: an application of Tus-Ter mediated protein microarray system. Methods Mol Biol 723:185-200
-
(2011)
Methods Mol Biol
, vol.723
, pp. 185-200
-
-
Sitaraman, K.1
Chatterjee, D.K.2
-
31
-
-
54749111053
-
Protein microarray on-demand: A novel protein microarray system
-
Chatterjee DK, Sitaraman K, Baptista C, Hartley J, Hill TM, Munroe DJ 2008 Protein microarray on-demand: a novel protein microarray system. PLoS One 3:e3265
-
(2008)
PLoS One
, vol.3
-
-
Chatterjee, D.K.1
Sitaraman, K.2
Baptista, C.3
Hartley, J.4
Hill, T.M.5
Munroe, D.J.6
-
32
-
-
84862874922
-
Emerging technology of in situ cell free expression protein microarrays
-
Nand A, Gautam A, Pérez JB, Merino A, Zhu J 2012 Emerging technology of in situ cell free expression protein microarrays. Protein Cell 3:84-88
-
(2012)
Protein Cell
, vol.3
, pp. 84-88
-
-
Nand, A.1
Gautam, A.2
Pérez, J.B.3
Merino, A.4
Zhu, J.5
-
33
-
-
10644230916
-
Current two-dimensional electrophoresis technology for proteomics
-
Görg A, Weiss W, Dunn MJ 2004 Current two-dimensional electrophoresis technology for proteomics. Proteomics 4:3665-3685
-
(2004)
Proteomics
, vol.4
, pp. 3665-3685
-
-
Görg, A.1
Weiss, W.2
Dunn, M.J.3
-
34
-
-
34248180415
-
Two-dimensional difference gel electrophoresis
-
Viswanathan S, Unlü M, Minden JS 2006 Two-dimensional difference gel electrophoresis. Nat Protoc 1:1351-1358
-
(2006)
Nat Protoc
, vol.1
, pp. 1351-1358
-
-
Viswanathan, S.1
Unlü, M.2
Minden, J.S.3
-
35
-
-
21244495253
-
The development of the DIGE system: 2D fluorescence difference gel analysis technology
-
Marouga R, David S, Hawkins E 2005 The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem 382:669-678
-
(2005)
Anal Bioanal Chem
, vol.382
, pp. 669-678
-
-
Marouga, R.1
David, S.2
Hawkins, E.3
-
36
-
-
0037253267
-
A novel experimental design for comparative twodimensional gel analysis: Two-dimensional difference gel electrophoresis incorporating a pooled internal standard
-
Alban A, David SO, Bjorkesten L, Andersson C, Sloge E, Lewis S, Currie I 2003 A novel experimental design for comparative twodimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3:36-44
-
(2003)
Proteomics
, vol.3
, pp. 36-44
-
-
Alban, A.1
David, S.O.2
Bjorkesten, L.3
Andersson, C.4
Sloge, E.5
Lewis, S.6
Currie, I.7
-
37
-
-
70349795274
-
Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport
-
Kosako H, Yamaguchi N, Aranami C, Ushiyama M, Kose S, Imamoto N, Taniguchi H, Nishida E, Hattori S 2009 Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport. Nat Struct Mol Biol 16: 1026-1035
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 1026-1035
-
-
Kosako, H.1
Yamaguchi, N.2
Aranami, C.3
Ushiyama, M.4
Kose, S.5
Imamoto, N.6
Taniguchi, H.7
Nishida, E.8
Hattori, S.9
-
38
-
-
29544444603
-
Efficient enrichment of intact phosphorylated proteins by modified immobilized metal-affinity chromatography
-
Dubrovska A, Souchelnytskyi S 2005 Efficient enrichment of intact phosphorylated proteins by modified immobilized metal-affinity chromatography. Proteomics 5:4678-4683
-
(2005)
Proteomics
, vol.5
, pp. 4678-4683
-
-
Dubrovska, A.1
Souchelnytskyi, S.2
-
39
-
-
0037435030
-
Mass spectrometry-based proteomics
-
Aebersold R, Mann M 2003 Mass spectrometry-based proteomics. Nature 422:198-207
-
(2003)
Nature
, vol.422
, pp. 198-207
-
-
Aebersold, R.1
Mann, M.2
-
40
-
-
8344284323
-
A common open representation of mass spectrometry data and its application to proteomics research
-
Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R 2004 A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 22:1459-1466
-
(2004)
Nat Biotechnol
, vol.22
, pp. 1459-1466
-
-
Pedrioli, P.G.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, 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..
-
41
-
-
66749171697
-
Statistical design of quantitative mass spectrometry-based proteomic experiments
-
Oberg AL, Vitek O 2009 Statistical design of quantitative mass spectrometry-based proteomic experiments. J Proteome Res 8:2144-2156
-
(2009)
J Proteome Res
, vol.8
, pp. 2144-2156
-
-
Oberg, A.L.1
Vitek, O.2
-
42
-
-
34250372908
-
Stable isotope labeling by amino acids in cell culture for quantitative proteomics
-
Ong SE, Mann M 2007 Stable isotope labeling by amino acids in cell culture for quantitative proteomics. Methods Mol Biol 359: 37-52
-
(2007)
Methods Mol Biol
, vol.359
, pp. 37-52
-
-
Ong, S.E.1
Mann, M.2
-
43
-
-
33746408762
-
The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation
-
von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD 2003 The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation. Mol Cell Proteomics 2:428-442
-
(2003)
Mol Cell Proteomics
, vol.2
, pp. 428-442
-
-
von Haller, P.D.1
Yi, E.2
Donohoe, S.3
Vaughn, K.4
Keller, A.5
Nesvizhskii, A.I.6
Eng, J.7
Li, X.J.8
Goodlett, D.R.9
Aebersold, R.10
Watts, J.D.11
-
44
-
-
33746432742
-
The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts
-
von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD 2003 The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts. Mol Cell Proteomics 2:426-427
-
(2003)
Mol Cell Proteomics
, vol.2
, pp. 426-427
-
-
von Haller, P.D.1
Yi, E.2
Donohoe, S.3
Vaughn, K.4
Keller, A.5
Nesvizhskii, A.I.6
Eng, J.7
Li, X.J.8
Goodlett, D.R.9
Aebersold, R.10
Watts, J.D.11
-
45
-
-
33646269941
-
A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies
-
Zieske LR 2006 A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies. J Exp Bot 57: 1501-1508
-
(2006)
J Exp Bot
, vol.57
, pp. 1501-1508
-
-
Zieske, L.R.1
-
46
-
-
77954366021
-
Quantitative analysis of mTRAQ-labeled proteome using full MS scans
-
Kang UB, Yeom J, Kim H, Lee C 2010 Quantitative analysis of mTRAQ-labeled proteome using full MS scans. J Proteome Res 9:3750-3758
-
(2010)
J Proteome Res
, vol.9
, pp. 3750-3758
-
-
Kang, U.B.1
Yeom, J.2
Kim, H.3
Lee, C.4
-
47
-
-
0024438708
-
Electrospray ionization for mass spectrometry of large biomolecules
-
Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM 1989 Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64-71
-
(1989)
Science
, vol.246
, pp. 64-71
-
-
Fenn, J.B.1
Mann, M.2
Meng, C.K.3
Wong, S.F.4
Whitehouse, C.M.5
-
48
-
-
84984042980
-
Protein and polymer analysis up to m/z 100,000 by laser ionization time-offlight mass spectrometry
-
Tanaka K, Ido Y, Akita S, Yoshida Y, Yoshida T 1988 Protein and polymer analysis up to m/z 100,000 by laser ionization time-offlight mass spectrometry. Rapid Commun Mass Spectrom 2:151
-
(1988)
Rapid Commun Mass Spectrom
, vol.2
, pp. 151
-
-
Tanaka, K.1
Ido, Y.2
Akita, S.3
Yoshida, Y.4
Yoshida, T.5
-
49
-
-
33845379876
-
Influence of the wavelength in high irradiance ultraviolet laser desorption mass spectrometry of organic molecules
-
Karas M, Bachmann, D., and Hillenkamp, F 1985 Influence of the wavelength in high irradiance ultraviolet laser desorption mass spectrometry of organic molecules. Anal Chem 57:2935-2939
-
(1985)
Anal Chem
, vol.57
, pp. 2935-2939
-
-
Karas, M.1
Bachmann, D.2
Hillenkamp, F.3
-
50
-
-
0029758906
-
Ligand induction of a transcriptionally active thyroid hormone receptor coactivator complex
-
Fondell JD, Ge H, Roeder RG 1996 Ligand induction of a transcriptionally active thyroid hormone receptor coactivator complex. Proc Natl Acad Sci USA 93:8329-8333
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 8329-8333
-
-
Fondell, J.D.1
Ge, H.2
Roeder, R.G.3
-
51
-
-
0032525781
-
A novel protein complex that interacts with the vitamin D3 receptor in a ligand-dependent manner and enhances VDR transactivation in a cell-free system
-
Rachez C, Suldan Z, Ward J, Chang CP, Burakov D, Erdjument-Bromage H, Tempst P, Freedman LP 1998 A novel protein complex that interacts with the vitamin D3 receptor in a ligand-dependent manner and enhances VDR transactivation in a cell-free system. Genes Dev 12:1787-1800
-
(1998)
Genes Dev
, vol.12
, pp. 1787-1800
-
-
Rachez, C.1
Suldan, Z.2
Ward, J.3
Chang, C.P.4
Burakov, D.5
Erdjument-Bromage, H.6
Tempst, P.7
Freedman, L.P.8
-
52
-
-
78650360165
-
Identification of proteins associated with ligand-activated estrogen receptor _ in human breast cancer cell nuclei by tandem affinity purification and nano LC-MS/M
-
Tarallo R, Bamundo A, Nassa G, Nola E, Paris O, Ambrosino C, Facchiano A, Baumann M, Nyman TA, Weisz A 2011 Identification of proteins associated with ligand-activated estrogen receptor _ in human breast cancer cell nuclei by tandem affinity purification and nano LC-MS/MS. Proteomics 11:172-179
-
(2011)
Proteomic
, vol.1
, pp. 172-179
-
-
Tarallo, R.1
Bamundo, A.2
Nassa, G.3
Nola, E.4
Paris, O.5
Ambrosino, C.6
Facchiano, A.7
Baumann, M.8
Nyman, T.A.9
Weisz, A.10
-
53
-
-
79959593177
-
Proteomic analysis of pathways involved in estrogen-induced growth and apoptosis of breast cancer cells
-
Hu ZZ, Kagan BL, Ariazi EA, Rosenthal DS, Zhang L, Li JV, Huang H, Wu C, Jordan VC, Riegel AT, Wellstein A 2011 Proteomic analysis of pathways involved in estrogen-induced growth and apoptosis of breast cancer cells. PLoS One 6:e20410
-
(2011)
PLoS One
, vol.6
-
-
Hu, Z.Z.1
Kagan, B.L.2
Ariazi, E.A.3
Rosenthal, D.S.4
Zhang, L.5
Li, J.V.6
Huang, H.7
Wu, C.8
Jordan, V.C.9
Riegel, A.T.10
Wellstein, A.11
-
54
-
-
33845207315
-
Proteomic analysis of MCF-7 breast cancer cell line exposed to mitogenic concentration of 17β-estradiol
-
Malorni L, Cacace G, Cuccurullo M, Pocsfalvi G, Chambery A, Farina A, Di Maro A, Parente A, Malorni A 2006 Proteomic analysis of MCF-7 breast cancer cell line exposed to mitogenic concentration of 17β-estradiol. Proteomics 6:5973-5982
-
(2006)
Proteomics
, vol.6
, pp. 5973-5982
-
-
Malorni, L.1
Cacace, G.2
Cuccurullo, M.3
Pocsfalvi, G.4
Chambery, A.5
Farina, A.6
Di Maro, A.7
Parente, A.8
Malorni, A.9
-
55
-
-
79957575162
-
Analysis of the human endogenous coregulator complexome
-
Malovannaya A, Lanz RB, Jung SY, Bulynko Y, Le NT, Chan DW, Ding C, Shi Y, Yucer N, Krenciute G, Kim BJ, Li C, Chen R, Li W, Wang Y, O'Malley BW, Qin J 2011 Analysis of the human endogenous coregulator complexome. Cell 145:787-799
-
(2011)
Cell
, vol.145
, pp. 787-799
-
-
Malovannaya, A.1
Lanz, R.B.2
Jung, S.Y.3
Bulynko, Y.4
Le, N.T.5
Chan, D.W.6
Ding, C.7
Shi, Y.8
Yucer, N.9
Krenciute, G.10
Kim, B.J.11
Li, C.12
Chen, R.13
Li, W.14
Wang, Y.15
O'Malley, B.W.16
Qin, J.17
-
56
-
-
76749140070
-
A comparison of proteomic profiles changes during 17_-estradiol treatment in human prostate cancer PC-3 cell line
-
Chen J, Huang P, Kaku H, Zhang K, Watanabe M, Saika T, Nasu Y, Kumon H 2009 A comparison of proteomic profiles changes during 17_-estradiol treatment in human prostate cancer PC-3 cell line. Cancer Genomics Proteomics 6:331-335
-
(2009)
Cancer Genomics Proteomics
, vol.6
, pp. 331-335
-
-
Chen, J.1
Huang, P.2
Kaku, H.3
Zhang, K.4
Watanabe, M.5
Saika, T.6
Nasu, Y.7
Kumon, H.8
-
57
-
-
38449089795
-
Estradiol in vivo regulation of brain mitochondrial proteome
-
Nilsen J, Irwin RW, Gallaher TK, Brinton RD 2007 Estradiol in vivo regulation of brain mitochondrial proteome. J Neurosci 27: 14069-14077
-
(2007)
J Neurosci
, vol.27
, pp. 14069-14077
-
-
Nilsen, J.1
Irwin, R.W.2
Gallaher, T.K.3
Brinton, R.D.4
-
58
-
-
7244247384
-
Shotgun sequence assem-bly and recent segmental duplications within the human genome
-
She X, Jiang Z, Clark RA, Liu G, Cheng Z, Tuzun E, Church DM, Sutton G, Halpern AL, Eichler EE 2004 Shotgun sequence assem-bly and recent segmental duplications within the human genome. Nature 431:927-930
-
(2004)
Nature
, vol.431
, pp. 927-930
-
-
She, X.1
Jiang, Z.2
Clark, R.A.3
Liu, G.4
Cheng, Z.5
Tuzun, E.6
Church, D.M.7
Sutton, G.8
Halpern, A.L.9
Eichler, E.E.10
-
59
-
-
20844440723
-
Identification of coexpressed gene clusters in a comparative analysis of transcriptome and proteome in mouse tissues
-
Mijalski T, Harder A, Halder T, Kersten M, Horsch M, Strom TM, Liebscher HV, Lottspeich F, de Angelis MH, Beckers J 2005 Identification of coexpressed gene clusters in a comparative analysis of transcriptome and proteome in mouse tissues. Proc Natl Acad Sci USA 102:8621-8626
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 8621-8626
-
-
Mijalski, T.1
Harder, A.2
Halder, T.3
Kersten, M.4
Horsch, M.5
Strom, T.M.6
Liebscher, H.V.7
Lottspeich, F.8
de Angelis, M.H.9
Beckers, J.10
-
60
-
-
0025817801
-
Dopamine activation of an orphan of the steroid receptor superfamily
-
Power RF, Lydon JP, Conneely OM, O'Malley BW 1991 Dopamine activation of an orphan of the steroid receptor superfamily. Science 252:1546-1548
-
(1991)
Science
, vol.252
, pp. 1546-1548
-
-
Power, R.F.1
Lydon, J.P.2
Conneely, O.M.3
O'Malley, B.W.4
-
61
-
-
0025043196
-
Hormonal regulation and identification of chicken progesterone receptor phosphorylation sites
-
Denner LA, Schrader WT, O'Malley BW, Weigel NL 1990 Hormonal regulation and identification of chicken progesterone receptor phosphorylation sites. J Biol Chem 265:16548-16555
-
(1990)
J Biol Chem
, vol.265
, pp. 16548-16555
-
-
Denner, L.A.1
Schrader, W.T.2
O'Malley, B.W.3
Weigel, N.L.4
-
63
-
-
63049112424
-
Systematic mapping of posttranslational modifications in human estrogen receptor-_ with emphasis on novel phosphorylation site
-
Atsriku C, Britton DJ, Held JM, Schilling B, Scott GK, Gibson BW, Benz CC, Baldwin MA 2009 Systematic mapping of posttranslational modifications in human estrogen receptor-_ with emphasis on novel phosphorylation sites. Mol Cell Proteomics 8:467-480
-
(2009)
Mol Cell Proteomic
, vol.8
, pp. 467-480
-
-
Atsriku, C.1
Britton, D.J.2
Held, J.M.3
Schilling, B.4
Scott, G.K.5
Gibson, B.W.6
Benz, C.C.7
Baldwin, M.A.8
-
64
-
-
79952384301
-
Quantitative phosphoproteomics studies using stable isotope dimethyl labeling coupled with IMAC-HILIC-nanoLC-MS/MS for estrogen-induced transcriptional regulation
-
Wu CJ, Chen YW, Tai JH, Chen SH 2011 Quantitative phosphoproteomics studies using stable isotope dimethyl labeling coupled with IMAC-HILIC-nanoLC-MS/MS for estrogen-induced transcriptional regulation. J Proteome Res 10:1088-1097
-
(2011)
J Proteome Res
, vol.10
, pp. 1088-1097
-
-
Wu, C.J.1
Chen, Y.W.2
Tai, J.H.3
Chen, S.H.4
-
65
-
-
78650934534
-
Integrated quantitative analysis of the phosphoproteome and transcriptome in tamoxifen-resistant breast cancer
-
Oyama M, Nagashima T, Suzuki T, Kozuka-Hata H, Yumoto N, Shiraishi Y, Ikeda K, Kuroki Y, Gotoh N, Ishida T, Inoue S, Kitano H, Okada-Hatakeyama M 2011 Integrated quantitative analysis of the phosphoproteome and transcriptome in tamoxifen-resistant breast cancer. J Biol Chem 286:818-829
-
(2011)
J Biol Chem
, vol.286
, pp. 818-829
-
-
Oyama, M.1
Nagashima, T.2
Suzuki, T.3
Kozuka-Hata, H.4
Yumoto, N.5
Shiraishi, Y.6
Ikeda, K.7
Kuroki, Y.8
Gotoh, N.9
Ishida, T.10
Inoue, S.11
Kitano, H.12
Okada-Hatakeyama, M.13
-
66
-
-
70350443849
-
Proteomic analysis of phosphorylated nuclear proteins underscores novel roles for rapid actions of retinoic acid in the regulation of mRNA splicing and translation
-
Laserna EJ, Valero ML, Sanz L, del Pino MM, Calvete JJ, Barettino D 2009 Proteomic analysis of phosphorylated nuclear proteins underscores novel roles for rapid actions of retinoic acid in the regulation of mRNA splicing and translation. Mol Endocrinol 23:1799-1814
-
(2009)
Mol Endocrinol
, vol.23
, pp. 1799-1814
-
-
Laserna, E.J.1
Valero, M.L.2
Sanz, L.3
del Pino, M.M.4
Calvete, J.J.5
Barettino, D.6
-
67
-
-
3242793327
-
Historical review: A brief history and personal retrospective of seven-transmembrane receptors
-
Lefkowitz RJ 2004 Historical review: a brief history and personal retrospective of seven-transmembrane receptors. Trends Pharmacol Sci 25:413-422
-
(2004)
Trends Pharmacol Sci
, vol.25
, pp. 413-422
-
-
Lefkowitz, R.J.1
-
68
-
-
56749170664
-
Proteomic identification and functional validation of activins and bone morphogenetic protein 11 as candidate novel muscle mass regulators
-
Souza TA, Chen X, Guo Y, Sava P, Zhang J, Hill JJ, Yaworsky PJ, Qiu Y 2008 Proteomic identification and functional validation of activins and bone morphogenetic protein 11 as candidate novel muscle mass regulators. Mol Endocrinol 22:2689-2702
-
(2008)
Mol Endocrinol
, vol.22
, pp. 2689-2702
-
-
Souza, T.A.1
Chen, X.2
Guo, Y.3
Sava, P.4
Zhang, J.5
Hill, J.J.6
Yaworsky, P.J.7
Qiu, Y.8
-
69
-
-
84856717660
-
Human CCAAT/enhancer-binding protein _ interacts with chromatin remodeling complexes of the imitation switch subfamily
-
Steinberg XP, Hepp MI, Fernández García Y, Suganuma T, Swanson SK, Washburn M, Workman JL, Gutiérrez JL 2012 Human CCAAT/enhancer-binding protein _ interacts with chromatin remodeling complexes of the imitation switch subfamily. Biochemistry 51:952-962
-
(2012)
Biochemistry
, vol.51
, pp. 952-962
-
-
Steinberg, X.P.1
Hepp, M.I.2
Fernández, G.Y.3
Suganuma, T.4
Swanson, S.K.5
Washburn, M.6
Workman, J.L.7
Gutiérrez, J.L.8
-
70
-
-
68149124471
-
Proteomic analysis of the mouse ovary in response to two gonadotropins, follicle-stimulating hormone and luteinizing hormone
-
Satoh M, Tokoro M, Ikegami H, Nagai K, Sono Y, Shin SW, Nishikawa S, Saeki K, Hosoi Y, Iritani A, Fukuda A, Morimoto Y, Matsumoto K 2009 Proteomic analysis of the mouse ovary in response to two gonadotropins, follicle-stimulating hormone and luteinizing hormone. J Reprod Dev 55:316-326
-
(2009)
J Reprod Dev
, vol.55
, pp. 316-326
-
-
Satoh, M.1
Tokoro, M.2
Ikegami, H.3
Nagai, K.4
Sono, Y.5
Shin, S.W.6
Nishikawa, S.7
Saeki, K.8
Hosoi, Y.9
Iritani, A.10
Fukuda, A.11
Morimoto, Y.12
Matsumoto, K.13
-
71
-
-
78650087650
-
Protein markers for insulin-producing _ cells with higher glucose sensitivity
-
Martens GA, Jiang L, Verhaeghen K, Connolly JB, Geromanos SG, Stangé G, Van Oudenhove L, Devreese B, Hellemans KH, Ling Z, Van Schravendijk C, Pipeleers DG, Vissers JP, Gorus FK 2010 Protein markers for insulin-producing _ cells with higher glucose sensitivity. PLoS One 5:e14214
-
(2010)
PLoS One
, vol.5
-
-
Martens, G.A.1
Jiang, L.2
Verhaeghen, K.3
Connolly, J.B.4
Geromanos, S.G.5
Stangé, G.6
van Oudenhove, L.7
Devreese, B.8
Hellemans, K.H.9
Ling, Z.10
van Schravendijk, C.11
Pipeleers, D.G.12
Vissers, J.P.13
Gorus, F.K.14
-
72
-
-
15744364422
-
Identification of parathyroid hormone-regulated proteins in mouse bone marrow cells by proteomics
-
Kim SH, Jun S, Jang HS, Lim SK 2005 Identification of parathyroid hormone-regulated proteins in mouse bone marrow cells by proteomics. Biochem Biophys Res Commun 330:423-429
-
(2005)
Biochem Biophys Res Commun
, vol.330
, pp. 423-429
-
-
Kim, S.H.1
Jun, S.2
Jang, H.S.3
Lim, S.K.4
-
73
-
-
79961014854
-
Large-scale phosphosite quantification in tissues by a spike-in SILAC method
-
Monetti M, Nagaraj N, Sharma K, Mann M 2011 Large-scale phosphosite quantification in tissues by a spike-in SILAC method. Nat Methods 8:655-658
-
(2011)
Nat Methods
, vol.8
, pp. 655-658
-
-
Monetti, M.1
Nagaraj, N.2
Sharma, K.3
Mann, M.4
-
74
-
-
40649117198
-
Dissection of the insulin signaling pathway via quantitative phosphoproteomics
-
Krüger M, Kratchmarova I, Blagoev B, Tseng YH, Kahn CR, Mann M 2008 Dissection of the insulin signaling pathway via quantitative phosphoproteomics. Proc Natl Acad Sci USA 105: 2451-2456
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 2451-2456
-
-
Krüger, M.1
Kratchmarova, I.2
Blagoev, B.3
Tseng, Y.H.4
Kahn, C.R.5
Mann, M.6
-
75
-
-
77957272228
-
Quantitative phosphoproteomic analysis reveals cAMP/vasopressin-dependent signaling pathways in native renal thick ascending limb cells
-
Gunaratne R, Braucht DW, Rinschen MM, Chou CL, Hoffert JD, Pisitkun T, Knepper MA 2010 Quantitative phosphoproteomic analysis reveals cAMP/vasopressin-dependent signaling pathways in native renal thick ascending limb cells. Proc Natl Acad Sci USA 107:15653-15658
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 15653-15658
-
-
Gunaratne, R.1
Braucht, D.W.2
Rinschen, M.M.3
Chou, C.L.4
Hoffert, J.D.5
Pisitkun, T.6
Knepper, M.A.7
-
76
-
-
77949381906
-
Phosphoproteomic profiling reveals vasopressin-regulated phosphorylation sites in collecting duct
-
Bansal AD, Hoffert JD, Pisitkun T, Hwang S, Chou CL, Boja ES, Wang G, Knepper MA 2010 Phosphoproteomic profiling reveals vasopressin-regulated phosphorylation sites in collecting duct. J Am Soc Nephrol 21:303-315
-
(2010)
J Am Soc Nephrol
, vol.21
, pp. 303-315
-
-
Bansal, A.D.1
Hoffert, J.D.2
Pisitkun, T.3
Hwang, S.4
Chou, C.L.5
Boja, E.S.6
Wang, G.7
Knepper, M.A.8
-
77
-
-
84858016523
-
Exploring salivary proteomes in edentulous patients with type 2 diabetes
-
Border MB, Schwartz S, Carlson J, Dibble CF, Kohltfarber H, Offenbacher S, Buse JB, Bencharit S 2012 Exploring salivary proteomes in edentulous patients with type 2 diabetes. Mol Biosyst 8:1304-1310
-
(2012)
Mol Biosyst
, vol.8
, pp. 1304-1310
-
-
Border, M.B.1
Schwartz, S.2
Carlson, J.3
Dibble, C.F.4
Kohltfarber, H.5
Offenbacher, S.6
Buse, J.B.7
Bencharit, S.8
-
78
-
-
84855302577
-
Comparison of tear proteins between healthy and early diabetic retinopathy patients
-
Kim HJ, Kim PK, Yoo HS, Kim CW 2012 Comparison of tear proteins between healthy and early diabetic retinopathy patients. Clin Biochem 45:60-67
-
(2012)
Clin Biochem
, vol.45
, pp. 60-67
-
-
Kim, H.J.1
Kim, P.K.2
Yoo, H.S.3
Kim, C.W.4
-
79
-
-
84858751820
-
Quantitative analysis of proteins in the tear fluid of patients with diabetic retinopathy
-
Cssz É, Boross P, Csutak A, Berta A, Tóth F, Póliska S, Török Z, Tzsér J 2012 Quantitative analysis of proteins in the tear fluid of patients with diabetic retinopathy. J Proteomics 75:2196-2204
-
(2012)
J Proteomics
, vol.75
, pp. 2196-2204
-
-
Cssz, E.1
Boross, P.2
Csutak, A.3
Berta, A.4
Tóth, F.5
Póliska, S.6
Török, Z.7
Tzsér, J.8
-
80
-
-
80052772366
-
Characterization of human myotubes from type 2 diabetic and nondiabetic subjects using complementary quantitative mass spectrometric methods
-
M110.006650
-
Thingholm TE, Bak S, Beck-Nielsen H, Jensen ON, Gaster M 2011 Characterization of human myotubes from type 2 diabetic and nondiabetic subjects using complementary quantitative mass spectrometric methods. Mol Cell Proteomics 10:M110.006650
-
(2011)
Mol Cell Proteomics
, vol.10
-
-
Thingholm, T.E.1
Bak, S.2
Beck-Nielsen, H.3
Jensen, O.N.4
Gaster, M.5
-
81
-
-
84855185323
-
Targeted proteomics of isolated glomeruli from the kidneys of diabetic rats: Sorbin and SH3 domain containing 2 is a novel protein associated with diabetic nephropathy
-
Nakatani S, Kakehashi A, Ishimura E, Yamano S, Mori K, Wei M, Inaba M, Wanibuchi H 2011 Targeted proteomics of isolated glomeruli from the kidneys of diabetic rats: sorbin and SH3 domain containing 2 is a novel protein associated with diabetic nephropathy. Exp Diabetes Res 2011:9793
-
(2011)
Exp Diabetes Res
, vol.9793
, pp. 2011
-
-
Nakatani, S.1
Kakehashi, A.2
Ishimura, E.3
Yamano, S.4
Mori, K.5
Wei, M.6
Inaba, M.7
Wanibuchi, H.8
-
82
-
-
79960404942
-
Proteomic identification of vanin-1 as a marker of kidney damage in a rat model of type 1 diabetic nephropathy
-
Fugmann T, Borgia B, Révész C, Godó M, Forsblom C, Hamar P, Holthöfer H, Neri D, Roesli C 2011 Proteomic identification of vanin-1 as a marker of kidney damage in a rat model of type 1 diabetic nephropathy. Kidney Int 80:272-281
-
(2011)
Kidney Int
, vol.80
, pp. 272-281
-
-
Fugmann, T.1
Borgia, B.2
Révész, C.3
Godó, M.4
Forsblom, C.5
Hamar, P.6
Holthöfer, H.7
Neri, D.8
Roesli, C.9
-
83
-
-
80755168393
-
Supporting tool suite for production proteomics
-
Ma ZQ, Tabb DL, Burden J, Chambers MC, Cox MB, Cantrell MJ, Ham AJ, Litton MD, Oreto MR, Schultz WC, Sobecki SM, Tsui TY, Wernke GR, Liebler DC 2011 Supporting tool suite for production proteomics. Bioinformatics 27:3214-3215
-
(2011)
Bioinformatics
, vol.27
, pp. 3214-3215
-
-
Ma, Z.Q.1
Tabb, D.L.2
Burden, J.3
Chambers, M.C.4
Cox, M.B.5
Cantrell, M.J.6
Ham, A.J.7
Litton, M.D.8
Oreto, M.R.9
Schultz, W.C.10
Sobecki, S.M.11
Tsui, T.Y.12
Wernke, G.R.13
Liebler, D.C.14
-
84
-
-
84255200971
-
PRODIS: A proteomics data management system with support to experiment tracking
-
Faria-Campos A, Fernandes-Rausch H, Val C, Thorun P, Abreu V, Batista PH, Mendonca PH, Alves V, Rodrigues MR, Pimenta A, Franco G, Campos SV 2011 PRODIS: a proteomics data management system with support to experiment tracking. BMCGenomics 12(Suppl 4):S15
-
(2011)
BMCGenomics
, vol.12
, Issue.4 SUPPL.
-
-
Faria-Campos, A.1
Fernandes-Rausch, H.2
Val, C.3
Thorun, P.4
Abreu, V.5
Batista, P.H.6
Mendonca, P.H.7
Alves, V.8
Rodrigues, M.R.9
Pimenta, A.10
Franco, G.11
Campos, S.V.12
-
85
-
-
67049146471
-
Getting started in computational mass spectrometry-based proteomics
-
Vitek O 2009 Getting started in computational mass spectrometry-based proteomics. PLoS Comput Biol 5:e1000366
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Vitek, O.1
-
86
-
-
41349096900
-
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
-
Deutsch EW, Lam H, Aebersold R 2008 Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics 33:18-25
-
(2008)
Physiol Genomics
, vol.33
, pp. 18-25
-
-
Deutsch, E.W.1
Lam, H.2
Aebersold, R.3
-
87
-
-
35848929694
-
Analysis and validation of proteomic data generated by tandem mass spectrometry
-
Nesvizhskii AI, Vitek O, Aebersold R 2007 Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 4:787-797
-
(2007)
Nat Methods
, vol.4
, pp. 787-797
-
-
Nesvizhskii, A.I.1
Vitek, O.2
Aebersold, R.3
-
88
-
-
17844394177
-
Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry
-
Listgarten J, Emili A 2005 Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 4:419-434
-
(2005)
Mol Cell Proteomics
, vol.4
, pp. 419-434
-
-
Listgarten, J.1
Emili, A.2
-
89
-
-
78651082595
-
Mzml: A community standard for mass spectrometry data
-
R110.000133
-
Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Rompp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW 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
-
90
-
-
33947366516
-
Development and validation of a spectral library searching method for peptide identification from MS/MS
-
Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R 2007 Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7:655-667
-
(2007)
Proteomics
, vol.7
, 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
-
92
-
-
67650382229
-
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: The Amsterdam principles
-
Rodriguez H, Snyder M, Uhlén M, Andrews P, Beavis R, Borchers C, Chalkley RJ, Cho SY, Cottingham K, Dunn M, Dylag T, Edgar R, Hare P, Heck AJ, Hirsch RF, Kennedy K, Kolar P, Kraus HJ, Mallick P, Nesvizhskii A, Ping P, Pontén F, Yang L, Yates JR, Stein SE, et al. 2009 Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res 8:3689-3692
-
(2009)
J Proteome Res
, vol.8
, pp. 3689-3692
-
-
Rodriguez, H.1
Snyder, M.2
Uhlén, M.3
Andrews, P.4
Beavis, R.5
Borchers, C.6
Chalkley, R.J.7
Cho, S.Y.8
Cottingham, K.9
Dunn, M.10
Dylag, T.11
Edgar, R.12
Hare, P.13
Heck, A.J.14
Hirsch, R.F.15
Kennedy, K.16
Kolar, P.17
Kraus, H.J.18
Mallick, P.19
Nesvizhskii, A.20
Ping, P.21
Pontén, F.22
Yang, L.23
Yates, J.R.24
Stein, S.E.25
more..
-
93
-
-
79961230601
-
The International Proteomics Tutorial Programme: Reaching out to the next generation proteome scientists
-
James P, Marko-Varga GA 2011 The International Proteomics Tutorial Programme: reaching out to the next generation proteome scientists. J Proteome Res 10:3311-3312
-
(2011)
J Proteome Res
, vol.10
, pp. 3311-3312
-
-
James, P.1
Marko-Varga, G.A.2
-
94
-
-
84856473028
-
From proteomics data representation to public data flow: A report on the HUPO-PSI workshop September 2011, Geneva, Switzerland
-
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martinez-Bartolomé S, Vizcaíno JA, Hermjakob H 2012 From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland. Proteomics 12:351-355
-
(2012)
Proteomics
, vol.12
, pp. 351-355
-
-
Orchard, S.1
Albar, J.P.2
Deutsch, E.W.3
Eisenacher, M.4
Binz, P.A.5
Martinez-Bartolomé, S.6
Vizcaíno, J.A.7
Hermjakob, H.8
-
95
-
-
84863036408
-
Translational proteomics in neurodegenerative diseases-16th HUPO
-
BPP workshop September 5 Geneva, Switzerland
-
Gröttrup B, Böckmann M, Stephan C, Marcus K, Grinberg LT, Meyer HE, Park YM 2012 Translational proteomics in neurodegenerative diseases-16th HUPO BPP workshop September 5, 2011 Geneva, Switzerland. Proteomics 12:356-358
-
(2011)
Proteomics
, vol.12
, pp. 356-358
-
-
Gröttrup, B.1
Böckmann, M.2
Stephan, C.3
Marcus, K.4
Grinberg, L.T.5
Meyer, H.E.6
Park, Y.M.7
-
96
-
-
84856490523
-
TheHUPOinitiative on Model Organism Proteomes, iMOP
-
Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, Hermjakob H, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, et al. 2012 TheHUPOinitiative on Model Organism Proteomes, iMOP. Proteomics 12:340-345
-
(2012)
Proteomics
, vol.12
, pp. 340-345
-
-
Jones, A.M.1
Aebersold, R.2
Ahrens, C.H.3
Apweiler, R.4
Baerenfaller, K.5
Baker, M.6
Bendixen, E.7
Briggs, S.8
Brownridge, P.9
Brunner, E.10
Daube, M.11
Deutsch, E.W.12
Grossniklaus, U.13
Heazlewood, J.14
Hengartner, M.O.15
Hermjakob, H.16
Jovanovic, M.17
Lawless, C.18
Lochnit, G.19
Martens, L.20
Ravnsborg, C.21
Schrimpf, S.P.22
Shim, Y.H.23
Subasic, D.24
Tholey, A.25
more..
-
97
-
-
33847111543
-
Entering the implementation era: A report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA
-
Orchard S, Taylor CF, Jones P, Montechi-Palazzo L, Binz PA, Jones AR, Pizarro A, Julian Jr RK, Hermjakob H 2007 Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA. Proteomics 7:337-339
-
(2007)
Proteomics
, vol.7
, pp. 337-339
-
-
Orchard, S.1
Taylor, C.F.2
Jones, P.3
Montechi-Palazzo, L.4
Binz, P.A.5
Jones, A.R.6
Pizarro, A.7
Julian, R.K.8
Hermjakob, H.9
-
99
-
-
34249062964
-
The minimum information about a proteomics experiment (MIAPE)
-
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian Jr RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, et al. 2007 The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 25:887-893
-
(2007)
Nat Biotechnol
, vol.25
, pp. 887-893
-
-
Taylor, C.F.1
Paton, N.W.2
Lilley, K.S.3
Binz, P.A.4
Julian, R.K.5
Jones, A.R.6
Zhu, W.7
Apweiler, R.8
Aebersold, R.9
Deutsch, E.W.10
Dunn, M.J.11
Heck, A.J.12
Leitner, A.13
Macht, M.14
Mann, M.15
Martens, L.16
Neubert, T.A.17
Patterson, S.D.18
Ping, P.19
Seymour, S.L.20
Souda, P.21
Tsugita, A.22
Vandekerckhove, J.23
Vondriska, T.M.24
more..
-
100
-
-
34249107988
-
The minimum information required for reporting a molecular interaction experiment (MIMIx)
-
Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, et al. 2007 The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol 25:894-898
-
(2007)
Nat Biotechnol
, vol.25
, pp. 894-898
-
-
Orchard, S.1
Salwinski, L.2
Kerrien, S.3
Montecchi-Palazzi, L.4
Oesterheld, M.5
Stümpflen, V.6
Ceol, A.7
Chatr-Aryamontri, A.8
Armstrong, J.9
Woollard, P.10
Salama, J.J.11
Moore, S.12
Wojcik, J.13
Bader, G.D.14
Vidal, M.15
Cusick, M.E.16
Gerstein, M.17
Gavin, A.C.18
Superti-Furga, G.19
Greenblatt, J.20
Bader, J.21
Uetz, P.22
Tyers, M.23
Legrain, P.24
Fields, S.25
more..
-
101
-
-
42049114671
-
The HUPO proteomics standards initiative: Easing communication and minimizing data loss in a changing world
-
Orchard S, Hermjakob H 2008 The HUPO proteomics standards initiative: easing communication and minimizing data loss in a changing world. Brief Bioinform 9:166-173
-
(2008)
Brief Bioinform
, vol.9
, pp. 166-173
-
-
Orchard, S.1
Hermjakob, H.2
-
102
-
-
84855461974
-
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)
-
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, et al. 2012 Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics 12:11-20
-
(2012)
Proteomics
, vol.12
, pp. 11-20
-
-
Kinsinger, C.R.1
Apffel, J.2
Baker, M.3
Bian, X.4
Borchers, C.H.5
Bradshaw, R.6
Brusniak, M.Y.7
Chan, D.W.8
Deutsch, E.W.9
Domon, B.10
Gorman, J.11
Grimm, R.12
Hancock, W.13
Hermjakob, H.14
Horn, D.15
Hunter, C.16
Kolar, P.17
Kraus, H.J.18
Langen, H.19
Linding, R.20
Moritz, R.L.21
Omenn, G.S.22
Orlando, R.23
Pandey, A.24
Ping, P.25
more..
-
103
-
-
84859208501
-
Protein interaction data curation: The International Molecular Exchange (IMEx) consortium
-
Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, et al. 2012 Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods 9:345-350
-
(2012)
Nat Methods
, vol.9
, pp. 345-350
-
-
Orchard, S.1
Kerrien, S.2
Abbani, S.3
Aranda, B.4
Bhate, J.5
Bidwell, S.6
Bridge, A.7
Briganti, L.8
Brinkman, F.S.9
Cesareni, G.10
Chatr-Aryamontri, A.11
Chautard, E.12
Chen, C.13
Dumousseau, M.14
Goll, J.15
Hancock, R.E.16
Hannick, L.I.17
Jurisica, I.18
Khadake, J.19
Lynn, D.J.20
Mahadevan, U.21
Perfetto, L.22
Raghunath, A.23
Ricard-Blum, S.24
Roechert, B.25
more..
-
104
-
-
35348976204
-
Broadening Broadening the horizon-level 2.5 of the HUPO-PSI format for molecular interactions
-
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, et al. 2007 Broadening Broadening the horizon-level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol 5:44
-
(2007)
BMC Biol
, vol.5
, pp. 44
-
-
Kerrien, S.1
Orchard, S.2
Montecchi-Palazzi, L.3
Aranda, B.4
Quinn, A.F.5
Vinod, N.6
Bader, G.D.7
Xenarios, I.8
Wojcik, J.9
Sherman, D.10
Tyers, M.11
Salama, J.J.12
Moore, S.13
Ceol, A.14
Chatr-Aryamontri, A.15
Oesterheld, M.16
Stümpflen, V.17
Salwinski, L.18
Nerothin, J.19
Cerami, E.20
Cusick, M.E.21
Vidal, M.22
Gilson, M.23
Armstrong, J.24
Woollard, P.25
more..
-
105
-
-
41649106470
-
Submit your interaction data the IMEx way: A step by step guide to trouble-free deposition
-
Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H 2007 Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition. Proteomics 7(Suppl 1):28-34
-
(2007)
Proteomics
, vol.7
, Issue.1 SUPPL.
, pp. 28-34
-
-
Orchard, S.1
Kerrien, S.2
Jones, P.3
Ceol, A.4
Chatr-Aryamontri, A.5
Salwinski, L.6
Nerothin, J.7
Hermjakob, H.8
-
106
-
-
43049127826
-
PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows
-
Deutsch EW, Lam H, Aebersold R 2008 PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep 9:429-434
-
(2008)
EMBO Rep
, vol.9
, pp. 429-434
-
-
Deutsch, E.W.1
Lam, H.2
Aebersold, R.3
-
107
-
-
77449100000
-
Using the PRIDE proteomics identifications database for knowledge discovery and data analysis
-
Jones P, Martens L 2010 Using the PRIDE proteomics identifications database for knowledge discovery and data analysis. Methods Mol Biol 604:297-307
-
(2010)
Methods Mol Biol
, vol.604
, pp. 297-307
-
-
Jones, P.1
Martens, L.2
-
109
-
-
79952196987
-
Data management and data integration in the HUPO plasma proteome project
-
Omenn GS 2011 Data management and data integration in the HUPO plasma proteome project. Methods Mol Biol 696:247-257
-
(2011)
Methods Mol Biol
, vol.696
, pp. 247-257
-
-
Omenn, G.S.1
-
110
-
-
3042735127
-
The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data
-
Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A 2004 The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics 3:531-533
-
(2004)
Mol Cell Proteomics
, vol.3
, pp. 531-533
-
-
Carr, S.1
Aebersold, R.2
Baldwin, M.3
Burlingame, A.4
Clauser, K.5
Nesvizhskii, A.6
-
111
-
-
31344448066
-
Guidelines for the next 10 years of proteomics
-
Wilkins MR, Appel RD, Van Eyk JE, Chung MC, Görg A, Hecker M, Huber LA, Langen H, Link AJ, Paik YK, Patterson SD, Pennington SR, Rabilloud T, Simpson RJ, Weiss W, Dunn MJ 2006 Guidelines for the next 10 years of proteomics. Proteomics 6:4-8
-
(2006)
Proteomics
, vol.6
, pp. 4-8
-
-
Wilkins, M.R.1
Appel, R.D.2
van Eyk, J.E.3
Chung, M.C.4
Görg, A.5
Hecker, M.6
Huber, L.A.7
Langen, H.8
Link, A.J.9
Paik, Y.K.10
Patterson, S.D.11
Pennington, S.R.12
Rabilloud, T.13
Simpson, R.J.14
Weiss, W.15
Dunn, M.J.16
-
112
-
-
33744926266
-
Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells
-
Unwin RD, Smith DL, Blinco D, Wilson CL, Miller CJ, Evans CA, Jaworska E, Baldwin SA, Barnes K, Pierce A, Spooncer E, Whetton AD 2006 Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells. Blood 107:4687-4694
-
(2006)
Blood
, vol.107
, pp. 4687-4694
-
-
Unwin, R.D.1
Smith, D.L.2
Blinco, D.3
Wilson, C.L.4
Miller, C.J.5
Evans, C.A.6
Jaworska, E.7
Baldwin, S.A.8
Barnes, K.9
Pierce, A.10
Spooncer, E.11
Whetton, A.D.12
-
115
-
-
33644527950
-
The model organism as a system: Integrating 'omics' data sets
-
Joyce AR, Palsson BØ 2006 The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol 7:198-210
-
(2006)
Nat Rev Mol Cell Biol
, vol.7
, pp. 198-210
-
-
Joyce, A.R.1
Palsson, B.O.2
-
116
-
-
78651328883
-
The BioGRID Interaction Database: 2011 update
-
Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M 2011 The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 39:D698-D704
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Stark, C.1
Breitkreutz, B.J.2
Chatr-Aryamontri, A.3
Boucher, L.4
Oughtred, R.5
Livstone, M.S.6
Nixon, J.7
van Auken, K.8
Wang, X.9
Shi, X.10
Reguly, T.11
Rust, J.M.12
Winter, A.13
Dolinski, K.14
Tyers, M.15
-
117
-
-
75549091794
-
MewesHW2010 CORUM: The comprehensive resource of mammalian protein complexes-2009
-
Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, MewesHW2010 CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Res 38:D497-D501
-
Nucleic Acids Res
, vol.38
-
-
Ruepp, A.1
Waegele, B.2
Lechner, M.3
Brauner, B.4
Dunger-Kaltenbach, I.5
Fobo, G.6
Frishman, G.7
Montrone, C.8
-
118
-
-
75549085083
-
Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology
-
Prasad TS, Kandasamy K, Pandey A 2009 Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods Mol Biol 577:67-79
-
(2009)
Methods Mol Biol
, vol.577
, pp. 67-79
-
-
Prasad, T.S.1
Kandasamy, K.2
Pandey, A.3
-
119
-
-
84858602406
-
InterPro in 2011: New developments in the family and domain prediction database
-
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, et al. 2012 InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 40:D306-D312
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Hunter, S.1
Jones, P.2
Mitchell, A.3
Apweiler, R.4
Attwood, T.K.5
Bateman, A.6
Bernard, T.7
Binns, D.8
Bork, P.9
Burge, S.10
de Castro, E.11
Coggill, P.12
Corbett, M.13
Das, U.14
Daugherty, L.15
Duquenne, L.16
Finn, R.D.17
Fraser, M.18
Gough, J.19
Haft, D.20
Hulo, N.21
Kahn, D.22
Kelly, E.23
Letunic, I.24
Lonsdale, D.25
more..
-
120
-
-
84862187489
-
Bairoch A 2012 neXtProt: A knowledge platform for human proteins
-
Lane L, Argoud-Puy G, Britan A, Cusin I, Duek PD, Evalet O, Gateau A, Gaudet P, Gleizes A, Masselot A, Zwahlen C, Bairoch A 2012 neXtProt: a knowledge platform for human proteins. Nucleic Acids Res 40:D76-D83
-
Nucleic Acids Res
, vol.40
-
-
Lane, L.1
Argoud-Puy, G.2
Britan, A.3
Cusin, I.4
Duek, P.D.5
Evalet, O.6
Gateau, A.7
Gaudet, P.8
Gleizes, A.9
Masselot, A.10
Zwahlen, C.11
-
121
-
-
84858077472
-
The Pfam protein families database
-
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD 2012 The Pfam protein families database. Nucleic Acids Res 40:D290-D301
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
Mistry, J.4
Tate, J.5
Boursnell, C.6
Pang, N.7
Forslund, K.8
Ceric, G.9
Clements, J.10
Heger, A.11
Holm, L.12
Sonnhammer, E.L.13
Eddy, S.R.14
Bateman, A.15
Finn, R.D.16
-
122
-
-
58149182728
-
PMAP: Databases for analyzing proteolytic events and pathways
-
Igarashi Y, Heureux E, Doctor KS, Talwar P, Gramatikova S, Gramatikoff K, Zhang Y, Blinov M, Ibragimova SS, Boyd S, Rat-nikov B, Cieplak P, Godzik A, Smith JW, Osterman AL, Eroshkin AM 2009 PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Res 37:D611-D618
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Igarashi, Y.1
Heureux, E.2
Doctor, K.S.3
Talwar, P.4
Gramatikova, S.5
Gramatikoff, K.6
Zhang, Y.7
Blinov, M.8
Ibragimova, S.S.9
Boyd, S.10
Rat-Nikov, B.11
Cieplak, P.12
Godzik, A.13
Smith, J.W.14
Osterman, A.L.15
Eroshkin, A.M.16
-
123
-
-
84860833500
-
Reorganizing the protein space at the Universal Protein Resource (UniProt)
-
UniProt Consortium
-
UniProt Consortium 2012 Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40:D71-D75
-
(2012)
Nucleic Acids Res
, vol.40
-
-
-
124
-
-
77951958243
-
CPFP: A central proteomics facilities pipeline
-
Trudgian DC, Thomas B, McGowan SJ, Kessler BM, Salek M, Acuto O 2010 CPFP: a central proteomics facilities pipeline. Bioinformatics 26:1131-1132
-
(2010)
Bioinformatics
, vol.26
, pp. 1131-1132
-
-
Trudgian, D.C.1
Thomas, B.2
McGowan, S.J.3
Kessler, B.M.4
Salek, M.5
Acuto, O.6
-
125
-
-
79952319218
-
IgraM2011 LabKey Server: An open source platform for scientific data integration, analysis and collaboration
-
Nelson EK, Piehler B, Eckels J, Rauch A, Bellew M, Hussey P, Ramsay S, Nathe C, Lum K, Krouse K, Stearns D, Connolly B, Skillman T, IgraM2011 LabKey Server: an open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics 12:71
-
BMC Bioinformatics
, vol.12
, pp. 71
-
-
Nelson, E.K.1
Piehler, B.2
Eckels, J.3
Rauch, A.4
Bellew, M.5
Hussey, P.6
Ramsay, S.7
Nathe, C.8
Lum, K.9
Krouse, K.10
Stearns, D.11
Connolly, B.12
Skillman, T.13
-
126
-
-
84861168275
-
OCAP: An open comprehensive analysis pipeline for iTRAQ
-
Wang P, Yang P, Yang JY 2012 OCAP: an open comprehensive analysis pipeline for iTRAQ. Bioinformatics 28:1404-1405
-
(2012)
Bioinformatics
, vol.28
, pp. 1404-1405
-
-
Wang, P.1
Yang, P.2
Yang, J.Y.3
-
127
-
-
77957190045
-
Integrated data management and validation platform for phosphorylated tandem mass spectrometry data
-
Lahesmaa-Korpinen AM, Carlson SM, White FM, Hautaniemi S 2010 Integrated data management and validation platform for phosphorylated tandem mass spectrometry data. Proteomics 10: 3515-3524
-
(2010)
Proteomics
, vol.10
, pp. 3515-3524
-
-
Lahesmaa-Korpinen, A.M.1
Carlson, S.M.2
White, F.M.3
Hautaniemi, S.4
-
128
-
-
33846706581
-
-
Kohlbacher O, Reinert K, Gröpl C, Lange E, Pfeifer N, Schulz-Trieglaff O, SturmM2007 TOPP: the OpenMS proteomics pipeline Bioinformatics 23:e191-e197
-
(2007)
TOPP: The OpenMS Proteomics Pipeline Bioinformatics
, vol.23
-
-
Kohlbacher, O.1
Reinert, K.2
Gröpl, C.3
Lange, E.4
Pfeifer, N.5
Schulz-Trieglaff, O.6
Sturm, M.7
-
129
-
-
33746930864
-
Aebersold R2005 A uniform proteomics MS/MS analysis platform utilizing open XML file formats
-
Keller A, Eng J, Zhang N, Li XJ, Aebersold R2005 A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol 1:2005.0017
-
(2005)
Mol Syst Biol
, vol.1
, pp. 0017
-
-
Keller, A.1
Eng, J.2
Zhang, N.3
Li, X.J.4
-
130
-
-
77949676526
-
A guided tour of the Trans-Proteomic Pipeline
-
Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, 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
-
131
-
-
0033434080
-
Probabilitybased protein identification by searching sequence databases using mass spectrometry data
-
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS 1999 Probabilitybased 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
Cottrell, J.S.4
-
132
-
-
7044246160
-
Open mass spectrometry search algorithm
-
Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH 2004 Open mass spectrometry search algorithm. J Proteome Res 3:958-964
-
(2004)
J Proteome Res
, vol.3
, 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
-
133
-
-
3042735333
-
High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics
-
Colinge J, Masselot A, Cusin I, Mahé E, Niknejad A, Argoud-Puy G, Reffas S, Bederr N, Gleizes A, Rey PA, Bougueleret L 2004 High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics 4:1977-1984
-
(2004)
Proteomics
, vol.4
, pp. 1977-1984
-
-
Colinge, J.1
Masselot, A.2
Cusin, I.3
Mahé, E.4
Niknejad, A.5
Argoud-Puy, G.6
Reffas, S.7
Bederr, N.8
Gleizes, A.9
Rey, P.A.10
Bougueleret, L.11
-
134
-
-
0036808207
-
ProbID: A probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data
-
Zhang N, Aebersold R, Schwikowski B 2002 ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics 2:1406-1412
-
(2002)
Proteomics
, vol.2
, pp. 1406-1412
-
-
Zhang, N.1
Aebersold, R.2
Schwikowski, B.3
-
135
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng JK, McCormack AL, Yates JR 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
-
136
-
-
3142702204
-
TANDEM: Matching proteins with tandem mass spectra
-
Craig R, Beavis RC 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
-
137
-
-
84855166719
-
MR-Tandem: Parallel XTandem using Hadoop MapReduce on Amazon Web Services
-
Pratt B, Howbert JJ, Tasman NI, Nilsson EJ 2012 MR-Tandem: parallel XTandem using Hadoop MapReduce on Amazon Web Services. Bioinformatics 28:136-137
-
(2012)
Bioinformatics
, vol.28
, pp. 136-137
-
-
Pratt, B.1
Howbert, J.J.2
Tasman, N.I.3
Nilsson, E.J.4
|