-
1
-
-
27644555055
-
Interpretation of shotgun proteomic data: the protein inference problem
-
Nesvizhskii A.I., Aebersold R. Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics 2005, 4:1419-1440.
-
(2005)
Mol Cell Proteomics
, vol.4
, pp. 1419-1440
-
-
Nesvizhskii, A.I.1
Aebersold, R.2
-
2
-
-
67349170059
-
A stress test for mass spectrometry-based proteomics
-
Aebersold R. A stress test for mass spectrometry-based proteomics. Nat Methods 2009, 6:411-412.
-
(2009)
Nat Methods
, vol.6
, pp. 411-412
-
-
Aebersold, R.1
-
3
-
-
77956304093
-
Mass spectrometry in high-throughput proteomics: ready for the big time
-
Nilsson T., Mann M., Aebersold R., Yates J.R., Bairoch A., Bergeron J.J. Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods 2010, 7:681-685.
-
(2010)
Nat Methods
, vol.7
, pp. 681-685
-
-
Nilsson, T.1
Mann, M.2
Aebersold, R.3
Yates, J.R.4
Bairoch, A.5
Bergeron, J.J.6
-
4
-
-
79952415252
-
Emerging molecular biomarkers-blood-based strategies to detect and monitor cancer
-
Hanash S.M., Baik C.S., Kallioniemi O. Emerging molecular biomarkers-blood-based strategies to detect and monitor cancer. Nat Rev Clin Oncol 2011, 8:142-150.
-
(2011)
Nat Rev Clin Oncol
, vol.8
, pp. 142-150
-
-
Hanash, S.M.1
Baik, C.S.2
Kallioniemi, O.3
-
5
-
-
0037434981
-
Disease proteomics
-
Hanash S. Disease proteomics. Nature 2003, 422:226-232.
-
(2003)
Nature
, vol.422
, pp. 226-232
-
-
Hanash, S.1
-
6
-
-
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., et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 2003, 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
-
7
-
-
19944432197
-
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
-
Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3:1154-1169.
-
(2004)
Mol Cell Proteomics
, vol.3
, pp. 1154-1169
-
-
Ross, P.L.1
Huang, Y.N.2
Marchese, J.N.3
Williamson, B.4
Parker, K.5
Hattan, S.6
-
8
-
-
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., Mann M. 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 2011, 10:1785-1793.
-
(2011)
J Proteome Res
, vol.10
, pp. 1785-1793
-
-
Michalski, A.1
Cox, J.2
Mann, M.3
-
9
-
-
77955455399
-
Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies
-
Houel S., Abernathy R., Renganathan K., Meyer-Arendt K., Ahn N.G., Old W.M. Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies. J Proteome Res 2010, 9:4152-4160.
-
(2010)
J Proteome Res
, vol.9
, pp. 4152-4160
-
-
Houel, S.1
Abernathy, R.2
Renganathan, K.3
Meyer-Arendt, K.4
Ahn, N.G.5
Old, W.M.6
-
10
-
-
77955462279
-
Addressing accuracy and precision issues in iTRAQ quantitation
-
Karp N.A., Huber W., Sadowski P.G., Charles P.D., Hester S.V., Lilley K.S. Addressing accuracy and precision issues in iTRAQ quantitation. Mol Cell Proteomics 2010, 9:1885-1897.
-
(2010)
Mol Cell Proteomics
, vol.9
, pp. 1885-1897
-
-
Karp, N.A.1
Huber, W.2
Sadowski, P.G.3
Charles, P.D.4
Hester, S.V.5
Lilley, K.S.6
-
11
-
-
52649098504
-
Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer
-
Bantscheff M., Boesche M., Eberhard D., Matthieson T., Sweetman G., Kuster B. Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer. Mol Cell Proteomics 2008, 7:1702-1713.
-
(2008)
Mol Cell Proteomics
, vol.7
, pp. 1702-1713
-
-
Bantscheff, M.1
Boesche, M.2
Eberhard, D.3
Matthieson, T.4
Sweetman, G.5
Kuster, B.6
-
12
-
-
70449412362
-
ITRAQ underestimation in simple and complex mixtures: "the good, the bad and the ugly"
-
Ow S.Y., Salim M., Noirel J., Evans C., Rehman I., Wright P.C. iTRAQ underestimation in simple and complex mixtures: "the good, the bad and the ugly". J Proteome Res 2009, 8:5347-5355.
-
(2009)
J Proteome Res
, vol.8
, pp. 5347-5355
-
-
Ow, S.Y.1
Salim, M.2
Noirel, J.3
Evans, C.4
Rehman, I.5
Wright, P.C.6
-
13
-
-
84883529394
-
Benchmarking stable isotope labeling based quantitative proteomics
-
Altelaar A.F., Frese C.K., Preisinger C., Hennrich M.L., Schram A.W., Timmers H.T., et al. Benchmarking stable isotope labeling based quantitative proteomics. J Proteomics 2013, 88:14-26.
-
(2013)
J Proteomics
, vol.88
, pp. 14-26
-
-
Altelaar, A.F.1
Frese, C.K.2
Preisinger, C.3
Hennrich, M.L.4
Schram, A.W.5
Timmers, H.T.6
-
14
-
-
84862333720
-
ITRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics
-
[M111 014423]
-
Mertins P., Udeshi N.D., Clauser K.R., Mani D.R., Patel J., Ong S.E., et al. iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics. Mol Cell Proteomics 2012, 11. [M111 014423].
-
(2012)
Mol Cell Proteomics
, vol.11
-
-
Mertins, P.1
Udeshi, N.D.2
Clauser, K.R.3
Mani, D.R.4
Patel, J.5
Ong, S.E.6
-
15
-
-
84862923173
-
Comprehensive comparison of iTRAQ and label-free LC-based quantitative proteomics approaches using two Chlamydomonas reinhardtii strains of interest for biofuels engineering
-
Wang H., Alvarez S., Hicks L.M. Comprehensive comparison of iTRAQ and label-free LC-based quantitative proteomics approaches using two Chlamydomonas reinhardtii strains of interest for biofuels engineering. J Proteome Res 2012, 11:487-501.
-
(2012)
J Proteome Res
, vol.11
, pp. 487-501
-
-
Wang, H.1
Alvarez, S.2
Hicks, L.M.3
-
16
-
-
79956270174
-
Minimising iTRAQ ratio compression through understanding LC-MS elution dependence and high-resolution HILIC fractionation
-
Ow S.Y., Salim M., Noirel J., Evans C., Wright P.C. Minimising iTRAQ ratio compression through understanding LC-MS elution dependence and high-resolution HILIC fractionation. Proteomics 2011, 11:2341-2346.
-
(2011)
Proteomics
, vol.11
, pp. 2341-2346
-
-
Ow, S.Y.1
Salim, M.2
Noirel, J.3
Evans, C.4
Wright, P.C.5
-
17
-
-
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., et al. 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 2011, 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
-
18
-
-
80155150331
-
Taming the isobaric tagging elephant in the room in quantitative proteomics
-
Christoforou A., Lilley K.S. Taming the isobaric tagging elephant in the room in quantitative proteomics. Nat Methods 2011, 8:911-913.
-
(2011)
Nat Methods
, vol.8
, pp. 911-913
-
-
Christoforou, A.1
Lilley, K.S.2
-
19
-
-
80155124832
-
MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics
-
Ting L., Rad R., Gygi S.P., Haas W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods 2011, 8:937-940.
-
(2011)
Nat Methods
, vol.8
, pp. 937-940
-
-
Ting, L.1
Rad, R.2
Gygi, S.P.3
Haas, W.4
-
20
-
-
80155205237
-
Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging
-
Wenger C.D., Lee M.V., Hebert A.S., McAlister G.C., Phanstiel D.H., Westphall M.S., et al. Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nat Methods 2011, 8:933-935.
-
(2011)
Nat Methods
, vol.8
, pp. 933-935
-
-
Wenger, C.D.1
Lee, M.V.2
Hebert, A.S.3
McAlister, G.C.4
Phanstiel, D.H.5
Westphall, M.S.6
-
21
-
-
84881163875
-
Measuring and managing ratio compression for accurate iTRAQ/TMT quantification
-
Savitski M.M., Mathieson T., Zinn N., Sweetman G., Doce C., Becher I., et al. Measuring and managing ratio compression for accurate iTRAQ/TMT quantification. J Proteome Res 2013, 12:3586-3598.
-
(2013)
J Proteome Res
, vol.12
, pp. 3586-3598
-
-
Savitski, M.M.1
Mathieson, T.2
Zinn, N.3
Sweetman, G.4
Doce, C.5
Becher, I.6
-
22
-
-
0036665581
-
Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry
-
Chelius D., Bondarenko P.V. Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res 2002, 1:317-323.
-
(2002)
J Proteome Res
, vol.1
, pp. 317-323
-
-
Chelius, D.1
Bondarenko, P.V.2
-
23
-
-
6044226889
-
Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures
-
Wiener M.C., Sachs J.R., Deyanova E.G., Yates N.A. Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal Chem 2004, 76:6085-6096.
-
(2004)
Anal Chem
, vol.76
, pp. 6085-6096
-
-
Wiener, M.C.1
Sachs, J.R.2
Deyanova, E.G.3
Yates, N.A.4
-
24
-
-
49749131566
-
Quantitative membrane proteomics applying narrow range peptide isoelectric focusing for studies of small cell lung cancer resistance mechanisms
-
Eriksson H., Lengqvist J., Hedlund J., Uhlen K., Orre L.M., Bjellqvist B., et al. Quantitative membrane proteomics applying narrow range peptide isoelectric focusing for studies of small cell lung cancer resistance mechanisms. Proteomics 2008, 8:3008-3018.
-
(2008)
Proteomics
, vol.8
, pp. 3008-3018
-
-
Eriksson, H.1
Lengqvist, J.2
Hedlund, J.3
Uhlen, K.4
Orre, L.M.5
Bjellqvist, B.6
-
25
-
-
34250349206
-
ITRAQ compatibility of peptide immobilized pH gradient isoelectric focusing
-
Lengqvist J., Uhlen K., Lehtio J. iTRAQ compatibility of peptide immobilized pH gradient isoelectric focusing. Proteomics 2007, 7:1746-1752.
-
(2007)
Proteomics
, vol.7
, pp. 1746-1752
-
-
Lengqvist, J.1
Uhlen, K.2
Lehtio, J.3
-
26
-
-
84864837496
-
Proteomic screen reveals Fbw7 as a modulator of the NF-kappaB pathway
-
Arabi A., Ullah K., Branca R.M., Johansson J., Bandarra D., Haneklaus M., et al. Proteomic screen reveals Fbw7 as a modulator of the NF-kappaB pathway. Nat Commun 2012, 3:976.
-
(2012)
Nat Commun
, vol.3
, pp. 976
-
-
Arabi, A.1
Ullah, K.2
Branca, R.M.3
Johansson, J.4
Bandarra, D.5
Haneklaus, M.6
-
27
-
-
70349974261
-
High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all
-
Kocher T., Pichler P., Schutzbier M., Stingl C., Kaul A., Teucher N., et al. High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all. J Proteome Res 2009, 8:4743-4752.
-
(2009)
J Proteome Res
, vol.8
, pp. 4743-4752
-
-
Kocher, T.1
Pichler, P.2
Schutzbier, M.3
Stingl, C.4
Kaul, A.5
Teucher, N.6
-
28
-
-
0000857494
-
An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database
-
Eng J.K., Mccormack A.L., Yates J.R. An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database. J Am Soc Mass Spectrom 1994, 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
-
29
-
-
35748972060
-
Semi-supervised learning for peptide identification from shotgun proteomics datasets
-
Kall L., Canterbury J.D., Weston J., Noble W.S., MacCoss M.J. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 2007, 4:923-925.
-
(2007)
Nat Methods
, vol.4
, pp. 923-925
-
-
Kall, L.1
Canterbury, J.D.2
Weston, J.3
Noble, W.S.4
MacCoss, M.J.5
-
30
-
-
57449099865
-
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
-
Cox J., Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008, 26:1367-1372.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1367-1372
-
-
Cox, J.1
Mann, M.2
-
31
-
-
76949097340
-
Quantitative proteomics reveals subset-specific viral recognition in dendritic cells
-
Luber C.A., Cox J., Lauterbach H., Fancke B., Selbach M., Tschopp J., et al. Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity 2010, 32:279-289.
-
(2010)
Immunity
, vol.32
, pp. 279-289
-
-
Luber, C.A.1
Cox, J.2
Lauterbach, H.3
Fancke, B.4
Selbach, M.5
Tschopp, J.6
-
32
-
-
79955436583
-
Quantitative analysis of the intra- and inter-individual variability of the normal urinary proteome
-
Nagaraj N., Mann M. Quantitative analysis of the intra- and inter-individual variability of the normal urinary proteome. J Proteome Res 2011, 10:637-645.
-
(2011)
J Proteome Res
, vol.10
, pp. 637-645
-
-
Nagaraj, N.1
Mann, M.2
-
33
-
-
84863724279
-
A proteomics approach reveals divergent molecular responses to salinity in populations of European whitefish (Coregonus lavaretus)
-
Papakostas S., Vasemagi A., Vaha J.P., Himberg M., Peil L., Primmer C.R. A proteomics approach reveals divergent molecular responses to salinity in populations of European whitefish (Coregonus lavaretus). Mol Ecol 2012, 21:3516-3530.
-
(2012)
Mol Ecol
, vol.21
, pp. 3516-3530
-
-
Papakostas, S.1
Vasemagi, A.2
Vaha, J.P.3
Himberg, M.4
Peil, L.5
Primmer, C.R.6
-
34
-
-
79953701087
-
Andromeda: a peptide search engine integrated into the MaxQuant environment
-
Cox J., Neuhauser N., Michalski A., Scheltema R.A., Olsen J.V., Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 2011, 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
-
35
-
-
56449107474
-
BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams
-
Hulsen T., de Vlieg J., Alkema W. BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. BMC Genomics 2008, 9:488.
-
(2008)
BMC Genomics
, vol.9
, pp. 488
-
-
Hulsen, T.1
de Vlieg, J.2
Alkema, W.3
-
36
-
-
84863230118
-
Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos
-
Li Z., Adams R.M., Chourey K., Hurst G.B., Hettich R.L., Pan C. Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos. J Proteome Res 2012, 11:1582-1590.
-
(2012)
J Proteome Res
, vol.11
, pp. 1582-1590
-
-
Li, Z.1
Adams, R.M.2
Chourey, K.3
Hurst, G.B.4
Hettich, R.L.5
Pan, C.6
-
37
-
-
77955159809
-
Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap
-
Pichler P., Kocher T., Holzmann J., Mazanek M., Taus T., Ammerer G., et al. Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap. Anal Chem 2010, 82:6549-6558.
-
(2010)
Anal Chem
, vol.82
, pp. 6549-6558
-
-
Pichler, P.1
Kocher, T.2
Holzmann, J.3
Mazanek, M.4
Taus, T.5
Ammerer, G.6
-
38
-
-
80855128111
-
The quantitative proteome of a human cell line
-
Beck M., Schmidt A., Malmstroem J., Claassen M., Ori A., Szymborska A., et al. The quantitative proteome of a human cell line. Mol Syst Biol 2011, 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
-
39
-
-
84874232489
-
The coming age of complete, accurate, and ubiquitous proteomes
-
Mann M., Kulak N.A., Nagaraj N., Cox J. The coming age of complete, accurate, and ubiquitous proteomes. Mol Cell 2013, 49:583-590.
-
(2013)
Mol Cell
, vol.49
, pp. 583-590
-
-
Mann, M.1
Kulak, N.A.2
Nagaraj, N.3
Cox, J.4
-
40
-
-
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., Mann M. Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics 2012, 11. [M111 014050].
-
(2012)
Mol Cell Proteomics
, vol.11
-
-
Geiger, T.1
Wehner, A.2
Schaab, C.3
Cox, J.4
Mann, M.5
-
41
-
-
78650642557
-
Defining the transcriptome and proteome in three functionally different human cell lines
-
Lundberg E., Fagerberg L., Klevebring D., Matic I., Geiger T., Cox J., et al. Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst Biol 2010, 6:450.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 450
-
-
Lundberg, E.1
Fagerberg, L.2
Klevebring, D.3
Matic, I.4
Geiger, T.5
Cox, J.6
-
42
-
-
84874762979
-
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
-
Vizcaino J.A., Côté R.G., Csordas A., Dianes J.A., Fabregat A., Foster J.M., et al. The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 2013, 41:D1063-D1069.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Vizcaino, J.A.1
Côté, R.G.2
Csordas, A.3
Dianes, J.A.4
Fabregat, A.5
Foster, J.M.6
|