-
1
-
-
84874805815
-
The challenge of the proteome dynamic range and its implications for in-depth proteomics
-
Zubarev RA (2013) The challenge of the proteome dynamic range and its implications for in-depth proteomics. Proteomics 13:723–726
-
(2013)
Proteomics
, vol.13
, pp. 723-726
-
-
Zubarev, R.A.1
-
2
-
-
71549132217
-
Isolation of subcellular organelles and structures
-
Michelsen U, von Hagen J (2009) Isolation of subcellular organelles and structures. Methods Enzymol 463:305–328
-
(2009)
Methods Enzymol
, vol.463
, pp. 305-328
-
-
Michelsen, U.1
Von Hagen, J.2
-
3
-
-
0035106351
-
Large-scale analysis of the yeast proteome by multidimensional protein identifi cation technology
-
Washburn MP, Wolters D, Yates JR 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identifi cation technology. Nat Biotechnol 19:242–247
-
(2001)
Nat Biotechnol
, vol.19
, pp. 242-247
-
-
Washburn, M.P.1
Wolters, D.2
Yates, J.R.3
-
4
-
-
0026694947
-
In-gel digestion of proteins for internal sequence analysis after one- or two- dimensional gel electrophoresis
-
Rosenfeld J, Capdevielle J, Guillemot JC et al (1992) In-gel digestion of proteins for internal sequence analysis after one- or two- dimensional gel electrophoresis. Anal Biochem 203:173–179
-
(1992)
Anal Biochem
, vol.203
, pp. 173-179
-
-
Rosenfeld, J.1
Capdevielle, J.2
Guillemot, J.C.3
-
5
-
-
0028983813
-
Improvement of an “In-Gel” digestion procedure for the micropreparation of internal protein fragments for amino acid sequencing
-
Hellman U, Wernstedt C, Góñez J et al (1995) Improvement of an “In-Gel” digestion procedure for the micropreparation of internal protein fragments for amino acid sequencing. Anal Biochem 224:451–455
-
(1995)
Anal Biochem
, vol.224
, pp. 451-455
-
-
Hellman, U.1
Wernstedt, C.2
Góñez, J.3
-
6
-
-
2542640024
-
Protein identifi cation by mass spectrometry
-
Baldwin MA (2004) Protein identifi cation by mass spectrometry. Mol Cell Proteomics 3:1–9
-
(2004)
Mol Cell Proteomics
, vol.3
, pp. 1-9
-
-
Baldwin, M.A.1
-
7
-
-
30144444853
-
Bioinformatic methods to exploit mass spectrometric data for proteomic applications
-
Chalkley RJ, Hansen KC, Baldwin MA (2005) Bioinformatic methods to exploit mass spectrometric data for proteomic applications. Methods Enzymol 402:289–312
-
(2005)
Methods Enzymol
, vol.402
, pp. 289-312
-
-
Chalkley, R.J.1
Hansen, K.C.2
Baldwin, M.A.3
-
8
-
-
54949129419
-
ProteoWizard: Open source software for rapid proteomics tools development. Bioinformatics (Oxford
-
Kessner D, Chambers M, Burke R et al (2008) ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics (Oxford, England) 24:2534–2536
-
(2008)
England)
, vol.24
, pp. 2534-2536
-
-
Kessner, D.1
Chambers, M.2
Burke, R.3
-
9
-
-
84876148755
-
Protein analysis by shotgun/bottom-up proteomics
-
Zhang Y, Fonslow BR, Shan B et al (2013) Protein analysis by shotgun/bottom-up proteomics. Chem Rev 113:2343–2394
-
(2013)
Chem Rev
, vol.113
, pp. 2343-2394
-
-
Zhang, Y.1
Fonslow, B.R.2
Shan, B.3
-
10
-
-
79952115268
-
Protein extraction from solid tissue. Methods Mol Biol (Clifton
-
Ericsson C, Nistér M (2011) Protein extraction from solid tissue. Methods Mol Biol (Clifton, NJ) 675:307–312
-
(2011)
NJ)
, vol.675
, pp. 307-312
-
-
Ericsson, C.1
Nistér, M.2
-
11
-
-
0345550275
-
Comparison of protein precipitation methods for sample preparation prior to proteomic analysis
-
Jiang L, He L, Fountoulakis M (2004) Comparison of protein precipitation methods for sample preparation prior to proteomic analysis. J Chromatogr A 1023:317–320
-
(2004)
J Chromatogr A
, vol.1023
, pp. 317-320
-
-
Jiang, L.1
He, L.2
Fountoulakis, M.3
-
12
-
-
0037444512
-
Fast-response proteomics by accelerated in-gel digestion of proteins
-
Havlis J, Thomas H, Sebela M et al (2003) Fast-response proteomics by accelerated in-gel digestion of proteins. Anal Chem 75: 1300–1306
-
(2003)
Anal Chem
, vol.75
, pp. 1300-1306
-
-
Havlis, J.1
Thomas, H.2
Sebela, M.3
-
13
-
-
0033434080
-
Probability-based protein identifi cation by searching sequence databases using mass spectrometry data
-
Perkins DN, Pappin DJ, Creasy DM et al (1999) Probability-based protein identifi cation 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
-
14
-
-
3142702204
-
TANDEM: Matching proteins with tandem mass spectra. Bioinformatics (Oxford
-
Craig R, Beavis RC (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics (Oxford, England) 20: 1466–1467
-
(2004)
England)
, vol.20
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
15
-
-
0033565832
-
Role of accurate mass measurement (+/− 10 ppm) in protein identifi cation strategies employing MS or MS/MS and database searching
-
Clauser KR, Baker P, Burlingame AL (1999) Role of accurate mass measurement (+/− 10 ppm) in protein identifi cation strategies employing MS or MS/MS and database searching. Anal Chem 71:2871–2882
-
(1999)
Anal Chem
, vol.71
, pp. 2871-2882
-
-
Clauser, K.R.1
Baker, P.2
Burlingame, A.L.3
-
16
-
-
24044487850
-
Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of- fl ight mass spectrometer: I. How much of the data is theoretically interpretable by search engines?
-
Chalkley RJ, Baker PR, Hansen KC et al (2005) Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of- fl ight mass spectrometer: I. How much of the data is theoretically interpretable by search engines? Mol Cell Proteomics MCP 4:1189–1193
-
(2005)
Mol Cell Proteomics MCP
, vol.4
, pp. 1189-1193
-
-
Chalkley, R.J.1
Baker, P.R.2
Hansen, K.C.3
-
17
-
-
24044491542
-
Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-fl ight mass spectrometer: II. New developments in protein prospector allow for reliable and comprehensive automatic analysis of large datasets
-
Chalkley RJ, Baker PR, Huang L et al (2005) Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-fl ight mass spectrometer: II. New developments in protein prospector allow for reliable and comprehensive automatic analysis of large datasets. Mol Cell Proteomics MCP 4:1194–1204
-
(2005)
Mol Cell Proteomics MCP
, vol.4
, pp. 1194-1204
-
-
Chalkley, R.J.1
Baker, P.R.2
Huang, L.3
-
18
-
-
0028920164
-
Effect of incubation of solutions of proteins containing dodecyl sulfate on the cleavage of peptide bonds by boiling
-
Kubo K (1995) Effect of incubation of solutions of proteins containing dodecyl sulfate on the cleavage of peptide bonds by boiling. Anal Biochem 225:351–353
-
(1995)
Anal Biochem
, vol.225
, pp. 351-353
-
-
Kubo, K.1
-
19
-
-
0026618996
-
Preincubation with cysteine prevents modifi cation of sulfhydryl groups in proteins by unreacted acrylamide in a gel
-
Chiari M, Righetti PG, Negri A et al (1992) Preincubation with cysteine prevents modifi cation of sulfhydryl groups in proteins by unreacted acrylamide in a gel. Electrophoresis 13: 882–884
-
(1992)
Electrophoresis
, vol.13
, pp. 882-884
-
-
Chiari, M.1
Righetti, P.G.2
Negri, A.3
-
20
-
-
0025893438
-
Selective precipitation of proteins from guanidine hydrochloridecontaining solutions with ethanol
-
Pepinsky RB (1991) Selective precipitation of proteins from guanidine hydrochloridecontaining solutions with ethanol. Anal biochem 195:177–181
-
(1991)
Anal Biochem
, vol.195
, pp. 177-181
-
-
Pepinsky, R.B.1
-
21
-
-
84865816264
-
Microwave-assisted protein staining, destaining, and in-gel/insolution digestion of proteins
-
(Clifton, NJ)
-
Lill JR, Nesatyy VJ (2012) Microwave-assisted protein staining, destaining, and in-gel/insolution digestion of proteins. Methods Mol Biol (Clifton, NJ) 869:521–532
-
(2012)
Methods Mol Biol
, vol.869
, pp. 521-532
-
-
Lill, J.R.1
Nesatyy, V.J.2
-
22
-
-
84863788092
-
Abnormal SDS-PAGE migration of cytosolic proteins can identify domains and mechanisms that control surfactant binding
-
Shi Y, Mowery RA, Ashley J et al (2012) Abnormal SDS-PAGE migration of cytosolic proteins can identify domains and mechanisms that control surfactant binding. Protein Sci 21:1197–1209
-
(2012)
Protein Sci
, vol.21
, pp. 1197-1209
-
-
Shi, Y.1
Mowery, R.A.2
Ashley, J.3
-
23
-
-
84857995363
-
Identifi cation of consistent alkylation of cysteine- less peptides in a proteomics experiment
-
Woods AG, Sokolowska I, Darie CC (2012) Identifi cation of consistent alkylation of cysteine- less peptides in a proteomics experiment. Biochem Biophys Res Commun 419: 305–308
-
(2012)
Biochem Biophys Res Commun
, vol.419
, pp. 305-308
-
-
Woods, A.G.1
Sokolowska, I.2
Darie, C.C.3
-
24
-
-
0037274605
-
Multiple enzymatic digestion for enhanced sequence coverage of proteins in complex proteomic mixtures using capillary LC with Ion trap MS/MS
-
Choudhary G, Wu S-L, Shieh P et al (2003) Multiple enzymatic digestion for enhanced sequence coverage of proteins in complex proteomic mixtures using capillary LC with Ion trap MS/MS. J Proteome Res 2:59–67
-
(2003)
J Proteome Res
, vol.2
, pp. 59-67
-
-
Choudhary, G.1
Wu, S.-L.2
Shieh, P.3
-
25
-
-
77949786295
-
Value of using multiple proteases for largescale mass spectrometry-based proteomics
-
Swaney DL, Wenger CD, Coon JJ (2010) Value of using multiple proteases for largescale mass spectrometry-based proteomics. J Proteome Res 9:1323–1329
-
(2010)
J Proteome Res
, vol.9
, pp. 1323-1329
-
-
Swaney, D.L.1
Wenger, C.D.2
Coon, J.J.3
-
26
-
-
0002844767
-
Systematic analysis of peptide recoveries from in-gel digestions for protein identifi cations in proteome studies
-
Speicher K, Kolbas O, Harper S et al (2000) Systematic analysis of peptide recoveries from in-gel digestions for protein identifi cations in proteome studies. J Biomol Tech JBT 11: 74–86
-
(2000)
J Biomol Tech JBT
, vol.11
, pp. 74-86
-
-
Speicher, K.1
Kolbas, O.2
Harper, S.3
-
27
-
-
84873038780
-
Effects of column and gradient lengths on peak capacity and peptide identifi cation in nanofl ow LC-MS/MS of complex proteomic samples
-
Hsieh EJ, Bereman MS, Durand S et al (2013) Effects of column and gradient lengths on peak capacity and peptide identifi cation in nanofl ow LC-MS/MS of complex proteomic samples. J Am Soc Mass Spectrom 24:148–153
-
(2013)
J am Soc Mass Spectrom
, vol.24
, pp. 148-153
-
-
Hsieh, E.J.1
Bereman, M.S.2
Durand, S.3
-
28
-
-
56149086397
-
Decision tree-driven tandem mass spectrometry for shotgun proteomics
-
Swaney DL, McAlister GC, Coon JJ (2008) Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat Methods 5:959–964
-
(2008)
Nat Methods
, vol.5
, pp. 959-964
-
-
Swaney, D.L.1
McAlister, G.C.2
Coon, J.J.3
|