-
1
-
-
0037435030
-
Mass spectrometry-based proteomics
-
Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207
-
(2003)
Nature
, vol.422
, pp. 198-207
-
-
Aebersold, R.1
Mann, M.2
-
3
-
-
80855128254
-
Deep proteome and transcriptome mapping of a human cancer cell line
-
Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Paabo, S., and Mann, M. (2011) Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 7, 548
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 548
-
-
Nagaraj, N.1
Wisniewski, J.R.2
Geiger, T.3
Cox, J.4
Kircher, M.5
Kelso, J.6
Paabo, S.7
Mann, M.8
-
4
-
-
84857938446
-
Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins
-
M111.014050
-
Geiger, T., Wehner, A., Schaab, C., Cox, J., and Mann, M. (2012) Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol. Cell. Proteomics M111.014050
-
(2012)
Mol. Cell. Proteomics
-
-
Geiger, T.1
Wehner, A.2
Schaab, C.3
Cox, J.4
Mann, M.5
-
5
-
-
80855128111
-
The quantitative proteome of a human cell line
-
Beck, M., Schmidt, A., Malmstroem, J., Claassen, M., Ori, A., Szymborska, A., Herzog, F., Rinner, O., Ellenberg, J., and Aebersold, R. (2011) The quantitative proteome of a human cell line. Mol. Syst. Biol. 7, 549
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 549
-
-
Beck, M.1
Schmidt, A.2
Malmstroem, J.3
Claassen, M.4
Ori, A.5
Szymborska, A.6
Herzog, F.7
Rinner, O.8
Ellenberg, J.9
Aebersold, R.10
-
6
-
-
27644555055
-
Interpretation of shotgun proteomic data: The protein inference problem
-
Nesvizhskii, A. I., and Aebersold, R. (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics 4, 1419-1440
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 1419-1440
-
-
Nesvizhskii, A.I.1
Aebersold, R.2
-
7
-
-
84868325438
-
SIMPATIQCO: A server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments
-
Pichler, P., Mazanek, M., Dusberger, F., Weilnbock, L., Huber, C. G., Stingl, C., Luider, T. M., Straube, W. L., Kocher, T., and Mechtler, K. (2012) SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments. J. Proteome Res. 11, 5540-5547
-
(2012)
J. Proteome Res.
, vol.11
, pp. 5540-5547
-
-
Pichler, P.1
Mazanek, M.2
Dusberger, F.3
Weilnbock, L.4
Huber, C.G.5
Stingl, C.6
Luider, T.M.7
Straube, W.L.8
Kocher, T.9
Mechtler, K.10
-
8
-
-
84861795226
-
SprayQc: A real-time LC-MS/MS quality monitoring system to maximize uptime using off the shelf components
-
Scheltema, R. A., and Mann, M. (2012) SprayQc: a real-time LC-MS/MS quality monitoring system to maximize uptime using off the shelf components. J. Proteome Res. 11, 3458-3466
-
(2012)
J. Proteome Res.
, vol.11
, pp. 3458-3466
-
-
Scheltema, R.A.1
Mann, M.2
-
9
-
-
84857991691
-
Systems-wide perturbation analysis with near complete coverage of the yeast proteome by single-shot UHPLC runs on a bench-top Orbitrap
-
M111.013722
-
Nagaraj, N., Kulak, N. A., Cox, J., Neuhaus, N., Mayr, K., Hoerning, O., Vorm, O., and Mann, M. (2011) Systems-wide perturbation analysis with near complete coverage of the yeast proteome by single-shot UHPLC runs on a bench-top Orbitrap. Mol. Cell. Proteomics, M111.013722
-
(2011)
Mol. Cell. Proteomics
-
-
Nagaraj, N.1
Kulak, N.A.2
Cox, J.3
Neuhaus, N.4
Mayr, K.5
Hoerning, O.6
Vorm, O.7
Mann, M.8
-
10
-
-
79953278916
-
Ultra-high-pressure RPLC hyphenated to an LTQ-Orbitrap Velos reveals a linear relation between peak capacity and number of identified peptides
-
Kocher, T., Swart, R., and Mechtler, K. (2011) Ultra-high-pressure RPLC hyphenated to an LTQ-Orbitrap Velos reveals a linear relation between peak capacity and number of identified peptides. Anal. Chem. 83, 2699-2704
-
(2011)
Anal. Chem.
, vol.83
, pp. 2699-2704
-
-
Kocher, T.1
Swart, R.2
Mechtler, K.3
-
11
-
-
80051624900
-
Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation
-
M110.003699
-
Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Frohlich, F., Cox, J., and Mann, M. (2011) Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol. Cell. Proteomics 10, M110.003699
-
(2011)
Mol. Cell. Proteomics
, vol.10
-
-
Thakur, S.S.1
Geiger, T.2
Chatterjee, B.3
Bandilla, P.4
Frohlich, F.5
Cox, J.6
Mann, M.7
-
12
-
-
84878633937
-
Orbitrap mass spectrometry
-
Zubarev, R. A., and Makarov, A. A. (2013) Orbitrap mass spectrometry. Anal. Chem. 85, 5288-5296
-
(2013)
Anal. Chem.
, vol.85
, pp. 5288-5296
-
-
Zubarev, R.A.1
Makarov, A.A.2
-
13
-
-
75149144996
-
A dual pressure linear ion trap orbitrap instrument with very high sequencing speed
-
Olsen, J. V., Schwartz, J. C., Griep-Raming, J., Nielsen, M. L., Damoc, E., Denisov, E., Lange, O., Remes, P., Taylor, D., Splendore, M., Wouters, E. R., Senko, M., Makarov, A., Mann, M., and Horning, S. (2009) A dual pressure linear ion trap orbitrap instrument with very high sequencing speed. Mol. Cell. Proteomics 8, 2759-2769
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 2759-2769
-
-
Olsen, J.V.1
Schwartz, J.C.2
Griep-Raming, J.3
Nielsen, M.L.4
Damoc, E.5
Denisov, E.6
Lange, O.7
Remes, P.8
Taylor, D.9
Splendore, M.10
Wouters, E.R.11
Senko, M.12
Makarov, A.13
Mann, M.14
Horning, S.15
-
14
-
-
80052769923
-
Mass spectrometry-based proteomics using Q exactive, a high-performance benchtop quadrupole orbitrap mass spectrometer
-
M111.011015
-
Michalski, A., Damoc, E., Hauschild, J. P., Lange, O., Wieghaus, A., Makarov, A., Nagaraj, N., Cox, J., Mann, M., and Horning, S. (2011) Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol. Cell. Proteomics 10, M111.011015
-
(2011)
Mol. Cell. Proteomics
, vol.10
-
-
Michalski, A.1
Damoc, E.2
Hauschild, J.P.3
Lange, O.4
Wieghaus, A.5
Makarov, A.6
Nagaraj, N.7
Cox, J.8
Mann, M.9
Horning, S.10
-
15
-
-
84870656540
-
Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer
-
Gallien, S., Duriez, E., Crone, C., Kellmann, M., Moehring, T., and Domon, B. (2012) Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Mol. Cell. Proteomics 11, 1709-1723
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 1709-1723
-
-
Gallien, S.1
Duriez, E.2
Crone, C.3
Kellmann, M.4
Moehring, T.5
Domon, B.6
-
16
-
-
84863393526
-
Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes
-
O111.013698
-
Michalski, A., Damoc, E., Lange, O., Denisov, E., Nolting, D., Mueller, M., Viner, R., Schwartz, J., Remes, P., Belford, M., Dunyach, J. J., Cox, J., Horning, S., Mann, M., and Makarov, A. (2011) Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes. Mol. Cell. Proteomics 11, O111.013698
-
(2011)
Mol. Cell. Proteomics
, vol.11
-
-
Michalski, A.1
Damoc, E.2
Lange, O.3
Denisov, E.4
Nolting, D.5
Mueller, M.6
Viner, R.7
Schwartz, J.8
Remes, P.9
Belford, M.10
Dunyach, J.J.11
Cox, J.12
Horning, S.13
Mann, M.14
Makarov, A.15
-
17
-
-
67349266694
-
Universal sample preparation method for proteome analysis
-
Wisniewski, J. R., Zougman, A., Nagaraj, N., and Mann, M. (2009) Universal sample preparation method for proteome analysis. Nat. Methods 6, 359-362
-
(2009)
Nat. Methods
, vol.6
, pp. 359-362
-
-
Wisniewski, J.R.1
Zougman, A.2
Nagaraj, N.3
Mann, M.4
-
18
-
-
0037317228
-
Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics
-
Rappsilber, J., Ishihama, Y., and Mann, M. (2003) Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75, 663-670
-
(2003)
Anal. Chem.
, vol.75
, pp. 663-670
-
-
Rappsilber, J.1
Ishihama, Y.2
Mann, M.3
-
19
-
-
57449099865
-
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
-
Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367-1372
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1367-1372
-
-
Cox, J.1
Mann, M.2
-
20
-
-
79953701087
-
Andromeda: A peptide search engine integrated into the MaxQuant environment
-
Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., and Mann, M. (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794-1805
-
(2011)
J. Proteome Res.
, vol.10
, pp. 1794-1805
-
-
Cox, J.1
Neuhauser, N.2
Michalski, A.3
Scheltema, R.A.4
Olsen, J.V.5
Mann, M.6
-
21
-
-
0030305457
-
R: A language for data analysis and graphics
-
Ihaka, R., and Gentleman, R. (1996) R: a language for data analysis and graphics. J. Comput. Graph. Stat. 299-314
-
(1996)
J. Comput. Graph. Stat.
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
-
23
-
-
84861860481
-
Targeted data extraction of the MS/MS spectra generated by data independent acquisition: A new concept for consistent and accurate proteome analysis
-
O111.016717
-
Gillet, L. C., Navarro, P., Tate, S., Roest, H., Selevsek, N., Reiter, L., Bonner, R., and Aebersold, R. (2012) Targeted data extraction of the MS/MS spectra generated by data independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 11, O111.016717
-
(2012)
Mol. Cell. Proteomics
, vol.11
-
-
Gillet, L.C.1
Navarro, P.2
Tate, S.3
Roest, H.4
Selevsek, N.5
Reiter, L.6
Bonner, R.7
Aebersold, R.8
-
24
-
-
79953719716
-
More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS
-
Michalski, A., Cox, J., and Mann, M. (2011) More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J. Proteome Res. 10, 1785-1793
-
(2011)
J. Proteome Res.
, vol.10
, pp. 1785-1793
-
-
Michalski, A.1
Cox, J.2
Mann, M.3
-
25
-
-
82555185589
-
Delayed fragmentation and optimized isolation width settings for improvement of protein identification and accuracy of isobaric mass tag quantification on Orbitrap-type mass spectrometers
-
Savitski, M. M., Sweetman, G., Askenazi, M., Marto, J. A., Lang, M., Zinn, N., and Bantscheff, M. (2011) Delayed fragmentation and optimized isolation width settings for improvement of protein identification and accuracy of isobaric mass tag quantification on Orbitrap-type mass spectrometers. Anal. Chem. 83, 8959-8967
-
(2011)
Anal. Chem.
, vol.83
, pp. 8959-8967
-
-
Savitski, M.M.1
Sweetman, G.2
Askenazi, M.3
Marto, J.A.4
Lang, M.5
Zinn, N.6
Bantscheff, M.7
-
26
-
-
12444345515
-
Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS
-
Thompson, A., Schafer, J., Kuhn, K., Kienle, S., Schwarz, J., Schmidt, G., Neumann, T., Johnstone, R., Mohammed, A. K., and Hamon, C. (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 75, 1895-1904
-
(2003)
Anal. Chem.
, vol.75
, pp. 1895-1904
-
-
Thompson, A.1
Schafer, J.2
Kuhn, K.3
Kienle, S.4
Schwarz, J.5
Schmidt, G.6
Neumann, T.7
Johnstone, R.8
Mohammed, A.K.9
Hamon, C.10
-
27
-
-
67650711335
-
Performance evaluation of a high-field Orbitrap mass analyzer
-
Makarov, A., Denisov, E., and Lange, O. (2009) Performance evaluation of a high-field Orbitrap mass analyzer. J. Am. Soc. Mass Spectrom. 20, 1391-1396
-
(2009)
J. Am. Soc. Mass Spectrom.
, vol.20
, pp. 1391-1396
-
-
Makarov, A.1
Denisov, E.2
Lange, O.3
-
28
-
-
84902126850
-
Enhanced fourier transform for orbitrap mass spectrometry
-
Lange, O., Damoc, E., Wieghaus, A., and Makarov, A. (2014) Enhanced Fourier transform for Orbitrap mass spectrometry. Int. J. Mass Spectrom. 369, 16-22
-
(2014)
Int. J. Mass Spectrom.
, vol.369
, pp. 16-22
-
-
Lange, O.1
Damoc, E.2
Wieghaus, A.3
Makarov, A.4
-
30
-
-
84884583449
-
Factorial experimental designs elucidate significant variables affecting data acquisition on a quadrupole Orbitrap mass spectrometer
-
Randall, S. M., Cardasis, H. L., and Muddiman, D. C. (2013) Factorial experimental designs elucidate significant variables affecting data acquisition on a quadrupole Orbitrap mass spectrometer. J. Am. Soc. Mass Spectrom. 24, 1501-1512
-
(2013)
J. Am. Soc. Mass Spectrom.
, vol.24
, pp. 1501-1512
-
-
Randall, S.M.1
Cardasis, H.L.2
Muddiman, D.C.3
-
31
-
-
84884903629
-
DMSO enhances electrospray response, boosting sensitivity of proteomic experiments
-
Hahne, H., Pachl, F., Ruprecht, B., Maier, S. K., Klaeger, S., Helm, D., Medard, G., Wilm, M., Lemeer, S., and Kuster, B. (2013) DMSO enhances electrospray response, boosting sensitivity of proteomic experiments. Nat. Methods 10, 989-991
-
(2013)
Nat. Methods
, vol.10
, pp. 989-991
-
-
Hahne, H.1
Pachl, F.2
Ruprecht, B.3
Maier, S.K.4
Klaeger, S.5
Helm, D.6
Medard, G.7
Wilm, M.8
Lemeer, S.9
Kuster, B.10
-
32
-
-
84910081742
-
A 'proteomic ruler' for protein copy number and concentration estimation without spike-in standards
-
M113.037309
-
Wioeniewski, J. R., Hein, M. Y., Cox, J., and Mann, M. (2014) A 'proteomic ruler' for protein copy number and concentration estimation without spike-in standards. Mol. Cell. Proteomics M113.037309
-
(2014)
Mol. Cell. Proteomics
-
-
Wioeniewski, J.R.1
Hein, M.Y.2
Cox, J.3
Mann, M.4
-
33
-
-
84861800006
-
Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole Orbitrap mass spectrometer
-
Kelstrup, C. D., Young, C., Lavallee, R., Nielsen, M. L., and Olsen, J. V. (2012) Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole Orbitrap mass spectrometer. J. Proteome Res. 11, 3487-3497
-
(2012)
J. Proteome Res.
, vol.11
, pp. 3487-3497
-
-
Kelstrup, C.D.1
Young, C.2
Lavallee, R.3
Nielsen, M.L.4
Olsen, J.V.5
-
34
-
-
84861906549
-
Nanoflow low pressure high peak capacity single dimension LC-MS/MS platform for high-throughput, in-depth analysis of mammalian proteomes
-
Zhou, F., Lu, Y., Ficarro, S. B., Webber, J. T., and Marto, J. A. (2012) Nanoflow low pressure high peak capacity single dimension LC-MS/MS platform for high-throughput, in-depth analysis of mammalian proteomes. Anal. Chem. 84, 5133-5139
-
(2012)
Anal. Chem.
, vol.84
, pp. 5133-5139
-
-
Zhou, F.1
Lu, Y.2
Ficarro, S.B.3
Webber, J.T.4
Marto, J.A.5
-
35
-
-
84889048480
-
From protein complexes to subunit backbone fragments: A multi-stage approach to native mass spectrometry
-
Belov, M. E., Damoc, E., Denisov, E., Compton, P. D., Horning, S., Makarov, A. A., and Kelleher, N. L. (2013) From protein complexes to subunit backbone fragments: a multi-stage approach to native mass spectrometry. Anal. Chem. 85, 11163-11173
-
(2013)
Anal. Chem.
, vol.85
, pp. 11163-11173
-
-
Belov, M.E.1
Damoc, E.2
Denisov, E.3
Compton, P.D.4
Horning, S.5
Makarov, A.A.6
Kelleher, N.L.7
|