-
1
-
-
23044510003
-
Preparation of 20-μm-i.d. Silica-based monolithic columns and their performance for proteomics analyses
-
DOI 10.1021/ac050454k
-
Q. Luo, Y. Shen, K.K. Hixson, R. Zhao, F. Yang, R.J. Moore, H.M. Mottaz, and R.D. Smith Preparation of 20-microm-i.d. silica-based monolithic columns and their performance for proteomics analyses Anal. Chem. 77 2005 5028 5035 (Pubitemid 41076696)
-
(2005)
Analytical Chemistry
, vol.77
, Issue.15
, pp. 5028-5035
-
-
Luo, Q.1
Shen, Y.2
Hixson, K.K.3
Zhao, R.4
Yang, F.5
Moore, R.J.6
Mottaz, H.M.7
Smith, R.D.8
-
2
-
-
77950420818
-
One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale
-
M. Iwasaki, S. Miwa, T. Ikegami, M. Tomita, N. Tanaka, and Y. Ishihama One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale Anal. Chem. 82 2010 2616 2620
-
(2010)
Anal. Chem.
, vol.82
, pp. 2616-2620
-
-
Iwasaki, M.1
Miwa, S.2
Ikegami, T.3
Tomita, M.4
Tanaka, N.5
Ishihama, Y.6
-
3
-
-
80051624900
-
Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation
-
(M110 003699)
-
S.S. Thakur, T. Geiger, B. Chatterjee, P. Bandilla, F. Frohlich, J. Cox, and M. Mann Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation Mol. Cell. Proteomics 10 2011 (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
-
4
-
-
80052769923
-
Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer
-
(M111 011015)
-
A. Michalski, E. Damoc, J.P. Hauschild, O. Lange, A. Wieghaus, A. Makarov, N. Nagaraj, J. Cox, M. Mann, and S. Horning Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer Mol. Cell. Proteomics 10 2011 (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
-
5
-
-
77954523086
-
Options and considerations when selecting a quantitative proteomics strategy
-
B. Domon, and R. Aebersold Options and considerations when selecting a quantitative proteomics strategy Nat. Biotechnol. 28 2010 710 721
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 710-721
-
-
Domon, B.1
Aebersold, R.2
-
6
-
-
19944432197
-
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
-
P.L. Ross, Y.N. Huang, J.N. Marchese, B. Williamson, K. Parker, S. Hattan, N. Khainovski, S. Pillai, S. Dey, S. Daniels, S. Purkayastha, P. Juhasz, S. Martin, M. Bartlet-Jones, F. He, A. Jacobson, and D.J. Pappin Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents Mol. Cell. Proteomics 3 2004 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
Khainovski, N.7
Pillai, S.8
Dey, S.9
Daniels, S.10
Purkayastha, S.11
Juhasz, P.12
Martin, S.13
Bartlet-Jones, M.14
He, F.15
Jacobson, A.16
Pappin, D.J.17
-
7
-
-
0036583926
-
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
-
S.E. Ong, B. Blagoev, I. Kratchmarova, D.B. Kristensen, H. Steen, A. Pandey, and M. Mann Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol. Cell. Proteomics 1 2002 376 386
-
(2002)
Mol. Cell. Proteomics
, vol.1
, pp. 376-386
-
-
Ong, S.E.1
Blagoev, B.2
Kratchmarova, I.3
Kristensen, D.B.4
Steen, H.5
Pandey, A.6
Mann, M.7
-
8
-
-
0037795741
-
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
-
DOI 10.1073/pnas.0832254100
-
S.A. Gerber, J. Rush, O. Stemman, M.W. Kirschner, and S.P. Gygi Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS Proc. Natl. Acad. Sci. U.S.A. 100 2003 6940 6945 (Pubitemid 36706372)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.12
, pp. 6940-6945
-
-
Gerber, S.A.1
Rush, J.2
Stemman, O.3
Kirschner, M.W.4
Gygi, S.P.5
-
9
-
-
57649218838
-
Stable isotopic labeling in proteomics
-
K. Gevaert, F. Impens, B. Ghesquiere, P. Van Damme, A. Lambrechts, and J. Vandekerckhove Stable isotopic labeling in proteomics Proteomics 8 2008 4873 4885
-
(2008)
Proteomics
, vol.8
, pp. 4873-4885
-
-
Gevaert, K.1
Impens, F.2
Ghesquiere, B.3
Van Damme, P.4
Lambrechts, A.5
Vandekerckhove, J.6
-
10
-
-
84870389523
-
Pipeline to assess the greatest source of technical variance in quantitative proteomics using metabolic labelling
-
M.R. Russell, and K.S. Lilley Pipeline to assess the greatest source of technical variance in quantitative proteomics using metabolic labelling J. Proteomics 77 2012 441 454
-
(2012)
J. Proteomics
, vol.77
, pp. 441-454
-
-
Russell, M.R.1
Lilley, K.S.2
-
11
-
-
79551500036
-
Less label, more free: Approaches in label-free quantitative mass spectrometry
-
K.A. Neilson, N.A. Ali, S. Muralidharan, M. Mirzaei, M. Mariani, G. Assadourian, A. Lee, S.C. van Sluyter, and P.A. Haynes Less label, more free: approaches in label-free quantitative mass spectrometry Proteomics 11 2011 535 553
-
(2011)
Proteomics
, vol.11
, pp. 535-553
-
-
Neilson, K.A.1
Ali, N.A.2
Muralidharan, S.3
Mirzaei, M.4
Mariani, M.5
Assadourian, G.6
Lee, A.7
Van Sluyter, S.C.8
Haynes, P.A.9
-
12
-
-
38649095599
-
An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data
-
DOI 10.1021/pr700758r
-
L.N. Mueller, M.Y. Brusniak, D.R. Mani, and R. Aebersold An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data J. Proteome Res. 7 2008 51 61 (Pubitemid 351171115)
-
(2008)
Journal of Proteome Research
, vol.7
, Issue.1
, pp. 51-61
-
-
Mueller, L.N.1
Brusniak, M.-Y.2
Mani, D.R.3
Aebersold, R.4
-
13
-
-
84867045160
-
Current challenges in software solutions for mass spectrometry-based quantitative proteomics
-
S. Cappadona, P.R. Baker, P.R. Cutillas, A.J. Heck, and B. van Breukelen Current challenges in software solutions for mass spectrometry-based quantitative proteomics Amino Acids 43 2012 1087 1108
-
(2012)
Amino Acids
, vol.43
, pp. 1087-1108
-
-
Cappadona, S.1
Baker, P.R.2
Cutillas, P.R.3
Heck, A.J.4
Van Breukelen, B.5
-
15
-
-
84860380761
-
Toward objective evaluation of proteomic algorithms
-
J.R. Yates III, S.K. Park, C.M. Delahunty, T. Xu, J.N. Savas, D. Cociorva, and P.C. Carvalho Toward objective evaluation of proteomic algorithms Nat. Methods 9 2012 455 456
-
(2012)
Nat. Methods
, vol.9
, pp. 455-456
-
-
Yates III, J.R.1
Park, S.K.2
Delahunty, C.M.3
Xu, T.4
Savas, J.N.5
Cociorva, D.6
Carvalho, P.C.7
-
16
-
-
27644543078
-
Comparison of label-free methods for quantifying human proteins by shotgun proteomics
-
DOI 10.1074/mcp.M500084-MCP200
-
W.M. Old, K. Meyer-Arendt, L. Aveline-Wolf, K.G. Pierce, A. Mendoza, J.R. Sevinsky, K.A. Resing, and N.G. Ahn Comparison of label-free methods for quantifying human proteins by shotgun proteomics Mol. Cell. Proteomics 4 2005 1487 1502 (Pubitemid 41555475)
-
(2005)
Molecular and Cellular Proteomics
, vol.4
, Issue.10
, pp. 1487-1502
-
-
Old, W.M.1
Meyer-Arendt, K.2
Aveline-Wolf, L.3
Pierce, K.G.4
Mendoza, A.5
Sevinsky, J.R.6
Resing, K.A.7
Ahn, N.G.8
-
17
-
-
84859611662
-
Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data
-
K. Ning, D. Fermin, and A.I. Nesvizhskii Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data J. Proteome Res. 11 2012 2261 2271
-
(2012)
J. Proteome Res.
, vol.11
, pp. 2261-2271
-
-
Ning, K.1
Fermin, D.2
Nesvizhskii, A.I.3
-
18
-
-
68449102172
-
Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans
-
J. Malmstrom, M. Beck, A. Schmidt, V. Lange, E.W. Deutsch, and R. Aebersold Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans Nature 460 2009 762 765
-
(2009)
Nature
, vol.460
, pp. 762-765
-
-
Malmstrom, J.1
Beck, M.2
Schmidt, A.3
Lange, V.4
Deutsch, E.W.5
Aebersold, R.6
-
19
-
-
33846165487
-
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
-
DOI 10.1038/nbt1270, PII NBT1270
-
P. Lu, C. Vogel, R. Wang, X. Yao, and E.M. Marcotte Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation Nat. Biotechnol. 25 2007 117 124 (Pubitemid 46087910)
-
(2007)
Nature Biotechnology
, vol.25
, Issue.1
, pp. 117-124
-
-
Lu, P.1
Vogel, C.2
Wang, R.3
Yao, X.4
Marcotte, E.M.5
-
20
-
-
74049132731
-
Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis
-
N.M. Griffin, J. Yu, F. Long, P. Oh, S. Shore, Y. Li, J.A. Koziol, and J.E. Schnitzer Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis Nat. Biotechnol. 28 2010 83 89
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 83-89
-
-
Griffin, N.M.1
Yu, J.2
Long, F.3
Oh, P.4
Shore, S.5
Li, Y.6
Koziol, J.A.7
Schnitzer, J.E.8
-
21
-
-
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
-
A. Michalski, J. Cox, and M. Mann 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 2011 1785 1793
-
(2011)
J. Proteome Res.
, vol.10
, pp. 1785-1793
-
-
Michalski, A.1
Cox, J.2
Mann, M.3
-
22
-
-
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)
-
A. Michalski, E. Damoc, O. Lange, E. Denisov, D. Nolting, M. Muller, R. Viner, J. Schwartz, P. Remes, M. Belford, J.J. Dunyach, J. Cox, S. Horning, M. Mann, and A. Makarov 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 2012 1 (O111 013698)
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 1
-
-
Michalski, A.1
Damoc, E.2
Lange, O.3
Denisov, E.4
Nolting, D.5
Muller, 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
-
23
-
-
79960578471
-
Quantification of mRNA and protein and integration with protein turnover in a bacterium
-
T. Maier, A. Schmidt, M. Guell, S. Kuhner, A.C. Gavin, R. Aebersold, and L. Serrano Quantification of mRNA and protein and integration with protein turnover in a bacterium Mol. Syst. Biol. 7 2011 511
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 511
-
-
Maier, T.1
Schmidt, A.2
Guell, M.3
Kuhner, S.4
Gavin, A.C.5
Aebersold, R.6
Serrano, L.7
-
24
-
-
79956322553
-
Global quantification of mammalian gene expression control
-
B. Schwanhausser, D. Busse, N. Li, G. Dittmar, J. Schuchhardt, J. Wolf, W. Chen, and M. Selbach Global quantification of mammalian gene expression control Nature 473 2011 337 342
-
(2011)
Nature
, vol.473
, pp. 337-342
-
-
Schwanhausser, B.1
Busse, D.2
Li, N.3
Dittmar, G.4
Schuchhardt, J.5
Wolf, J.6
Chen, W.7
Selbach, M.8
-
25
-
-
62149110095
-
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics
-
M.Y. Brusniak, B. Bodenmiller, D. Campbell, K. Cooke, J. Eddes, A. Garbutt, H. Lau, S. Letarte, L.N. Mueller, V. Sharma, O. Vitek, N. Zhang, R. Aebersold, and J.D. Watts Corra: computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics BMC Bioinformatics 9 2008 542
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 542
-
-
Brusniak, M.Y.1
Bodenmiller, B.2
Campbell, D.3
Cooke, K.4
Eddes, J.5
Garbutt, A.6
Lau, H.7
Letarte, S.8
Mueller, L.N.9
Sharma, V.10
Vitek, O.11
Zhang, N.12
Aebersold, R.13
Watts, J.D.14
-
26
-
-
57449099865
-
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
-
J. Cox, and M. Mann MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Nat. Biotechnol. 26 2008 1367 1372
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1367-1372
-
-
Cox, J.1
Mann, M.2
-
27
-
-
84862316959
-
MsCompare: A framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies
-
(M111 015974)
-
B. Hoekman, R. Breitling, F. Suits, R. Bischoff, and P. Horvatovich msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies Mol. Cell. Proteomics 11 2012 1 (M111 015974)
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 1
-
-
Hoekman, B.1
Breitling, R.2
Suits, F.3
Bischoff, R.4
Horvatovich, P.5
-
28
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
DOI 10.1101/gr.4086505
-
B. Giardine, C. Riemer, R.C. Hardison, R. Burhans, L. Elnitski, P. Shah, Y. Zhang, D. Blankenberg, I. Albert, J. Taylor, W. Miller, W.J. Kent, and A. Nekrutenko Galaxy: a platform for interactive large-scale genome analysis Genome Res. 15 2005 1451 1455 (Pubitemid 41400913)
-
(2005)
Genome Research
, vol.15
, Issue.10
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
Burhans, R.4
Elnitski, L.5
Shah, P.6
Zhang, Y.7
Blankenberg, D.8
Albert, I.9
Taylor, J.10
Miller, W.11
Kent, W.J.12
Nekrutenko, A.13
-
29
-
-
79960905787
-
Galaxy: A web-based genome analysis tool for experimentalists
-
(Chapter 19, Unit 19 10 11-21)
-
D. Blankenberg, G. Von Kuster, N. Coraor, G. Ananda, R. Lazarus, M. Mangan, A. Nekrutenko, and J. Taylor Galaxy: a web-based genome analysis tool for experimentalists Curr. Protoc. Mol. Biol. 1 1999 (Chapter 19, Unit 19 10 11-21)
-
(1999)
Curr. Protoc. Mol. Biol.
, vol.1
-
-
Blankenberg, D.1
Von Kuster, G.2
Coraor, N.3
Ananda, G.4
Lazarus, R.5
Mangan, M.6
Nekrutenko, A.7
Taylor, J.8
-
30
-
-
67049100049
-
The proteios software environment: An extensible multiuser platform for management and analysis of proteomics data
-
J. Hakkinen, G. Vincic, O. Mansson, K. Warell, and F. Levander The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data J. Proteome Res. 8 2009 3037 3043
-
(2009)
J. Proteome Res.
, vol.8
, pp. 3037-3043
-
-
Hakkinen, J.1
Vincic, G.2
Mansson, O.3
Warell, K.4
Levander, F.5
-
32
-
-
33846706581
-
TOPP - The OpenMS proteomics pipeline
-
O. Kohlbacher, K. Reinert, C. Gropl, E. Lange, N. Pfeifer, O. Schulz-Trieglaff, and M. Sturm TOPP - the OpenMS proteomics pipeline Bioinformatics 23 2007 e191 197
-
(2007)
Bioinformatics
, vol.23
, pp. 191-197
-
-
Kohlbacher, O.1
Reinert, K.2
Gropl, C.3
Lange, E.4
Pfeifer, N.5
Schulz-Trieglaff, O.6
Sturm, M.7
-
33
-
-
77449106982
-
OpenMS and TOPP: Open source software for LC-MS data analysis
-
K. Reinert, and O. Kohlbacher OpenMS and TOPP: open source software for LC-MS data analysis Methods Mol. Biol. 604 2010 201 211
-
(2010)
Methods Mol. Biol.
, vol.604
, pp. 201-211
-
-
Reinert, K.1
Kohlbacher, O.2
-
34
-
-
42249108173
-
OpenMS - An open-source software framework for mass spectrometry
-
M. Sturm, A. Bertsch, C. Gropl, A. Hildebrandt, R. Hussong, E. Lange, N. Pfeifer, O. Schulz-Trieglaff, A. Zerck, K. Reinert, and O. Kohlbacher OpenMS - an open-source software framework for mass spectrometry BMC Bioinformatics 9 2008 163
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 163
-
-
Sturm, M.1
Bertsch, A.2
Gropl, C.3
Hildebrandt, A.4
Hussong, R.5
Lange, E.6
Pfeifer, N.7
Schulz-Trieglaff, O.8
Zerck, A.9
Reinert, K.10
Kohlbacher, O.11
-
35
-
-
79953701087
-
Andromeda: A peptide search engine integrated into the MaxQuant environment
-
J. Cox, N. Neuhauser, A. Michalski, R.A. Scheltema, J.V. Olsen, and M. Mann Andromeda: a peptide search engine integrated into the MaxQuant environment J. Proteome Res. 10 2011 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
-
36
-
-
0141955057
-
A method for reducing the time required to match protein sequences with tandem mass spectra
-
R. Craig, and R.C. Beavis A method for reducing the time required to match protein sequences with tandem mass spectra Rapid Commun. Mass Spectrom. 17 2003 2310 2316 (Pubitemid 37243315)
-
(2003)
Rapid Communications in Mass Spectrometry
, vol.17
, Issue.20
, pp. 2310-2316
-
-
Craig, R.1
Beavis, R.C.2
-
37
-
-
7044246160
-
Open mass spectrometry search algorithm
-
DOI 10.1021/pr0499491
-
L.Y. Geer, S.P. Markey, J.A. Kowalak, L. Wagner, M. Xu, D.M. Maynard, X. Yang, W. Shi, and S.H. Bryant Open mass spectrometry search algorithm J. Proteome Res. 3 2004 958 964 (Pubitemid 39425651)
-
(2004)
Journal of Proteome Research
, vol.3
, Issue.5
, 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
-
38
-
-
0033434080
-
Probability-based protein identification by searching sequence databases using mass spectrometry data
-
D.N. Perkins, D.J. Pappin, D.M. Creasy, and J.S. Cottrell Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 20 1999 3551 3567 (Pubitemid 30007252)
-
(1999)
Electrophoresis
, vol.20
, Issue.18
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.C.2
Creasy, D.M.3
Cottrell, J.S.4
-
39
-
-
59849093889
-
Prediction of high-responding peptides for targeted protein assays by mass spectrometry
-
V.A. Fusaro, D.R. Mani, J.P. Mesirov, and S.A. Carr Prediction of high-responding peptides for targeted protein assays by mass spectrometry Nat. Biotechnol. 27 2009 190 198
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 190-198
-
-
Fusaro, V.A.1
Mani, D.R.2
Mesirov, J.P.3
Carr, S.A.4
-
40
-
-
80053074684
-
CONSeQuence: Prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches
-
(M110 003384)
-
C.E. Eyers, C. Lawless, D.C. Wedge, K.W. Lau, S.J. Gaskell, and S.J. Hubbard CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches Mol. Cell. Proteomics 10 2011 (M110 003384)
-
(2011)
Mol. Cell. Proteomics
, vol.10
-
-
Eyers, C.E.1
Lawless, C.2
Wedge, D.C.3
Lau, K.W.4
Gaskell, S.J.5
Hubbard, S.J.6
-
41
-
-
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)
-
L.C. Gillet, P. Navarro, S. Tate, H. Rost, N. Selevsek, L. Reiter, R. Bonner, and R. Aebersold 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 2012 (O111 016717)
-
(2012)
Mol. Cell. Proteomics
, vol.11
-
-
Gillet, L.C.1
Navarro, P.2
Tate, S.3
Rost, H.4
Selevsek, N.5
Reiter, L.6
Bonner, R.7
Aebersold, R.8
-
42
-
-
40549126588
-
Alignment of LC-MS images, with applications to biomarker discovery and protein identification
-
DOI 10.1002/pmic.200700791
-
M. Vandenbogaert, S. Li-Thiao-Te, H.M. Kaltenbach, R. Zhang, T. Aittokallio, and B. Schwikowski Alignment of LC-MS images, with applications to biomarker discovery and protein identification Proteomics 8 2008 650 672 (Pubitemid 351362928)
-
(2008)
Proteomics
, vol.8
, Issue.4
, pp. 650-672
-
-
Vandenbogaert, M.1
Li-Thiao-Te, S.2
Kaltenbach, H.-M.3
Zhang, R.4
Aittokallio, T.5
Schwikowski, B.6
-
43
-
-
41549117597
-
A quantitative analysis software tool for mass spectrometry-based proteomics
-
DOI 10.1038/nmeth.1195, PII NMETH.1195
-
S.K. Park, J.D. Venable, T. Xu, and J.R. Yates III A quantitative analysis software tool for mass spectrometry-based proteomics Nat. Methods 5 2008 319 322 (Pubitemid 351459367)
-
(2008)
Nature Methods
, vol.5
, Issue.4
, pp. 319-322
-
-
Park, S.K.1
Venable, J.D.2
Xu, T.3
Yates III, J.R.4
-
44
-
-
33845527323
-
ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces
-
DOI 10.1021/ac060923y
-
R.G. Sadygov, F.M. Maroto, and A.F. Huhmer ChromAlign: a two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces Anal. Chem. 78 2006 8207 8217 (Pubitemid 44927596)
-
(2006)
Analytical Chemistry
, vol.78
, Issue.24
, pp. 8207-8217
-
-
Sadygov, R.G.1
Maroto, F.M.2
Huhmer, A.F.R.3
-
45
-
-
55749105172
-
MS-BID: A Java package for label-free LC-MS-based comparative proteomic analysis
-
D. Hwang, N. Zhang, H. Lee, E. Yi, H. Zhang, I.Y. Lee, L. Hood, and R. Aebersold MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis Bioinformatics 24 2008 2641 2642
-
(2008)
Bioinformatics
, vol.24
, pp. 2641-2642
-
-
Hwang, D.1
Zhang, N.2
Lee, H.3
Yi, E.4
Zhang, H.5
Lee, I.Y.6
Hood, L.7
Aebersold, R.8
-
46
-
-
76649139789
-
IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation
-
C.C. Tsou, C.F. Tsai, Y.H. Tsui, P.R. Sudhir, Y.T. Wang, Y.J. Chen, J.Y. Chen, T.Y. Sung, and W.L. Hsu IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation Mol. Cell. Proteomics 9 2010 131 144
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 131-144
-
-
Tsou, C.C.1
Tsai, C.F.2
Tsui, Y.H.3
Sudhir, P.R.4
Wang, Y.T.5
Chen, Y.J.6
Chen, J.Y.7
Sung, T.Y.8
Hsu, W.L.9
-
47
-
-
33645463331
-
MapQuant: Open-source software for large-scale protein quantification
-
K.C. Leptos, D.A. Sarracino, J.D. Jaffe, B. Krastins, and G.M. Church MapQuant: open-source software for large-scale protein quantification Proteomics 6 2006 1770 1782
-
(2006)
Proteomics
, vol.6
, pp. 1770-1782
-
-
Leptos, K.C.1
Sarracino, D.A.2
Jaffe, J.D.3
Krastins, B.4
Church, G.M.5
-
48
-
-
80051817160
-
MassChroQ: A versatile tool for mass spectrometry quantification
-
B. Valot, O. Langella, E. Nano, and M. Zivy MassChroQ: a versatile tool for mass spectrometry quantification Proteomics 11 2011 3572 3577
-
(2011)
Proteomics
, vol.11
, pp. 3572-3577
-
-
Valot, B.1
Langella, O.2
Nano, E.3
Zivy, M.4
-
49
-
-
82955195935
-
MassUntangler: A novel alignment tool for label-free liquid chromatography-mass spectrometry proteomic data
-
R. Ballardini, M. Benevento, G. Arrigoni, L. Pattini, and A. Roda MassUntangler: a novel alignment tool for label-free liquid chromatography-mass spectrometry proteomic data J. Chromatogr. A 1218 2011 8859 8868
-
(2011)
J. Chromatogr. A
, vol.1218
, pp. 8859-8868
-
-
Ballardini, R.1
Benevento, M.2
Arrigoni, G.3
Pattini, L.4
Roda, A.5
-
50
-
-
14344250874
-
Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry
-
DOI 10.1074/mcp.M400061-MCP200
-
D. Radulovic, S. Jelveh, S. Ryu, T.G. Hamilton, E. Foss, Y. Mao, and A. Emili Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry Mol. Cell. Proteomics 3 2004 984 997 (Pubitemid 40361233)
-
(2004)
Molecular and Cellular Proteomics
, vol.3
, Issue.10
, pp. 984-997
-
-
Radulovic, D.1
Jelveh, S.2
Ryu, S.3
Hamilton, T.G.4
Foss, E.5
Mao, Y.6
Emili, A.7
-
51
-
-
42949157310
-
Two-dimensional method for time aligning liquid chromatography-mass spectrometry data
-
DOI 10.1021/ac702267h
-
F. Suits, J. Lepre, P. Du, R. Bischoff, and P. Horvatovich Two-dimensional method for time aligning liquid chromatography-mass spectrometry data Anal. Chem. 80 2008 3095 3104 (Pubitemid 351620693)
-
(2008)
Analytical Chemistry
, vol.80
, Issue.9
, pp. 3095-3104
-
-
Suits, F.1
Lepre, J.2
Du, P.3
Bischoff, R.4
Horvatovich, P.5
-
52
-
-
33747180294
-
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
-
DOI 10.1093/bioinformatics/btl276
-
M. Bellew, M. Coram, M. Fitzgibbon, M. Igra, T. Randolph, P. Wang, D. May, J. Eng, R. Fang, C. Lin, J. Chen, D. Goodlett, J. Whiteaker, A. Paulovich, and M. McIntosh A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS Bioinformatics 22 2006 1902 1909 (Pubitemid 44283036)
-
(2006)
Bioinformatics
, vol.22
, Issue.15
, pp. 1902-1909
-
-
Bellew, M.1
Coram, M.2
Fitzgibbon, M.3
Igra, M.4
Randolph, T.5
Wang, P.6
May, D.7
Eng, J.8
Fang, R.9
Lin, C.10
Chen, J.11
Goodlett, D.12
Whiteaker, J.13
Paulovich, A.14
McIntosh, M.15
-
53
-
-
73649131275
-
MSQuant, an open source platform for mass spectrometry-based quantitative proteomics
-
P. Mortensen, J.W. Gouw, J.V. Olsen, S.E. Ong, K.T. Rigbolt, J. Bunkenborg, J. Cox, L.J. Foster, A.J. Heck, B. Blagoev, J.S. Andersen, and M. Mann MSQuant, an open source platform for mass spectrometry-based quantitative proteomics J. Proteome Res. 9 2010 393 403
-
(2010)
J. Proteome Res.
, vol.9
, pp. 393-403
-
-
Mortensen, P.1
Gouw, J.W.2
Olsen, J.V.3
Ong, S.E.4
Rigbolt, K.T.5
Bunkenborg, J.6
Cox, J.7
Foster, L.J.8
Heck, A.J.9
Blagoev, B.10
Andersen, J.S.11
Mann, M.12
-
54
-
-
33644867564
-
MZmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data
-
DOI 10.1093/bioinformatics/btk039
-
M. Katajamaa, J. Miettinen, and M. Oresic MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data Bioinformatics 22 2006 634 636 (Pubitemid 43372832)
-
(2006)
Bioinformatics
, vol.22
, Issue.5
, pp. 634-636
-
-
Katajamaa, M.1
Miettinen, J.2
Oresic, M.3
-
55
-
-
25444526868
-
Processing methods for differential analysis of LC/MS profile data
-
M. Katajamaa, and M. Oresic Processing methods for differential analysis of LC/MS profile data BMC Bioinformatics 6 2005 179
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 179
-
-
Katajamaa, M.1
Oresic, M.2
-
56
-
-
77954772536
-
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
-
T. Pluskal, S. Castillo, A. Villar-Briones, and M. Oresic MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data BMC Bioinformatics 11 2010 395
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 395
-
-
Pluskal, T.1
Castillo, S.2
Villar-Briones, A.3
Oresic, M.4
-
57
-
-
33750615386
-
PEPPeR, a platform for experimental proteomic pattern recognition
-
DOI 10.1074/mcp.M600222-MCP200
-
J.D. Jaffe, D.R. Mani, K.C. Leptos, G.M. Church, M.A. Gillette, and S.A. Carr PEPPeR, a platform for experimental proteomic pattern recognition Mol. Cell. Proteomics 5 2006 1927 1941 (Pubitemid 44688201)
-
(2006)
Molecular and Cellular Proteomics
, vol.5
, Issue.10
, pp. 1927-1941
-
-
Jaffe, J.D.1
Mani, D.R.2
Leptos, K.C.3
Church, G.M.4
Gillette, M.A.5
Carr, S.A.6
-
58
-
-
70349436819
-
Protein quantification across hundreds of experimental conditions
-
Z. Khan, J.S. Bloom, B.A. Garcia, M. Singh, and L. Kruglyak Protein quantification across hundreds of experimental conditions Proc. Natl. Acad. Sci. U.S.A. 106 2009 15544 15548
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 15544-15548
-
-
Khan, Z.1
Bloom, J.S.2
Garcia, B.A.3
Singh, M.4
Kruglyak, L.5
-
59
-
-
79953306449
-
SIMA: Simultaneous multiple alignment of LC/MS peak lists
-
B. Voss, M. Hanselmann, B.Y. Renard, M.S. Lindner, U. Kothe, M. Kirchner, and F.A. Hamprecht SIMA: simultaneous multiple alignment of LC/MS peak lists Bioinformatics 27 2011 987 993
-
(2011)
Bioinformatics
, vol.27
, pp. 987-993
-
-
Voss, B.1
Hanselmann, M.2
Renard, B.Y.3
Lindner, M.S.4
Kothe, U.5
Kirchner, M.6
Hamprecht, F.A.7
-
60
-
-
84861178173
-
Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: Application to protein acetylation and phosphorylation
-
B. Schilling, M.J. Rardin, B.X. MacLean, A.M. Zawadzka, B.E. Frewen, M.P. Cusack, D.J. Sorensen, M.S. Bereman, E. Jing, C.C. Wu, E. Verdin, C.R. Kahn, M.J. Maccoss, and B.W. Gibson Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation Mol. Cell. Proteomics 11 2012 202 214
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 202-214
-
-
Schilling, B.1
Rardin, M.J.2
Maclean, B.X.3
Zawadzka, A.M.4
Frewen, B.E.5
Cusack, M.P.6
Sorensen, D.J.7
Bereman, M.S.8
Jing, E.9
Wu, C.C.10
Verdin, E.11
Kahn, C.R.12
Maccoss, M.J.13
Gibson, B.W.14
-
61
-
-
26844492976
-
A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry
-
DOI 10.1074/mcp.M500141-MCP200
-
X.J. Li, E.C. Yi, C.J. Kemp, H. Zhang, and R. Aebersold A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry Mol. Cell. Proteomics 4 2005 1328 1340 (Pubitemid 41448720)
-
(2005)
Molecular and Cellular Proteomics
, vol.4
, Issue.9
, pp. 1328-1340
-
-
Li, X.-J.1
Yi, E.C.2
Kemp, C.J.3
Zhang, H.4
Aebersold, R.5
-
62
-
-
35348965139
-
SuperHirn - A novel tool for high resolution LC-MS-based peptide/protein profiling
-
DOI 10.1002/pmic.200700057
-
L.N. Mueller, O. Rinner, A. Schmidt, S. Letarte, B. Bodenmiller, M.Y. Brusniak, O. Vitek, R. Aebersold, and M. Muller SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling Proteomics 7 2007 3470 3480 (Pubitemid 47597670)
-
(2007)
Proteomics
, vol.7
, Issue.19
, pp. 3470-3480
-
-
Mueller, L.N.1
Rinner, O.2
Schmidt, A.3
Letarte, S.4
Bodenmiller, B.5
Brusniak, M.-Y.6
Vitek, O.7
Aebersold, R.8
Muller, M.9
-
63
-
-
32444446805
-
XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification
-
DOI 10.1021/ac051437y
-
C.A. Smith, E.J. Want, G. O'Maille, R. Abagyan, and G. Siuzdak XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification Anal. Chem. 78 2006 779 787 (Pubitemid 43228585)
-
(2006)
Analytical Chemistry
, vol.78
, Issue.3
, pp. 779-787
-
-
Smith, C.A.1
Want, E.J.2
O'Maille, G.3
Abagyan, R.4
Siuzdak, G.5
-
64
-
-
50049096775
-
XCMS2: Processing tandem mass spectrometry data for metabolite identification and structural characterization
-
H.P. Benton, D.M. Wong, S.A. Trauger, and G. Siuzdak XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization Anal. Chem. 80 2008 6382 6389
-
(2008)
Anal. Chem.
, vol.80
, pp. 6382-6389
-
-
Benton, H.P.1
Wong, D.M.2
Trauger, S.A.3
Siuzdak, G.4
-
65
-
-
84861915827
-
XCMS Online: A web-based platform to process untargeted metabolomic data
-
R. Tautenhahn, G.J. Patti, D. Rinehart, and G. Siuzdak XCMS Online: a web-based platform to process untargeted metabolomic data Anal. Chem. 84 2012 5035 5039
-
(2012)
Anal. Chem.
, vol.84
, pp. 5035-5039
-
-
Tautenhahn, R.1
Patti, G.J.2
Rinehart, D.3
Siuzdak, G.4
-
66
-
-
0036665581
-
Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry
-
DOI 10.1021/pr025517j
-
D. Chelius, and P.V. Bondarenko Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry J. Proteome Res. 1 2002 317 323 (Pubitemid 36395872)
-
(2002)
Journal of Proteome Research
, vol.1
, Issue.4
, pp. 317-323
-
-
Chelius, D.1
Bondarenko, P.V.2
-
67
-
-
79952304665
-
Generic workflow for quality assessment of quantitative label-free LC-MS analysis
-
M. Sandin, M. Krogh, K. Hansson, and F. Levander Generic workflow for quality assessment of quantitative label-free LC-MS analysis Proteomics 11 2011 1114 1124
-
(2011)
Proteomics
, vol.11
, pp. 1114-1124
-
-
Sandin, M.1
Krogh, M.2
Hansson, K.3
Levander, F.4
-
68
-
-
79957847680
-
Combining quantitative proteomics data processing workflows for greater sensitivity
-
N. Colaert, C. Van Huele, S. Degroeve, A. Staes, J. Vandekerckhove, K. Gevaert, and L. Martens Combining quantitative proteomics data processing workflows for greater sensitivity Nat. Methods 8 2011 481 483
-
(2011)
Nat. Methods
, vol.8
, pp. 481-483
-
-
Colaert, N.1
Van Huele, C.2
Degroeve, S.3
Staes, A.4
Vandekerckhove, J.5
Gevaert, K.6
Martens, L.7
-
69
-
-
39049193622
-
High-accuracy peak picking of proteomics data using wavelet techniques
-
E. Lange, C. Gropl, K. Reinert, O. Kohlbacher, and A. Hildebrandt High-accuracy peak picking of proteomics data using wavelet techniques Pac. Symp. Biocomput. 2006 243 254
-
(2006)
Pac. Symp. Biocomput.
, pp. 243-254
-
-
Lange, E.1
Gropl, C.2
Reinert, K.3
Kohlbacher, O.4
Hildebrandt, A.5
-
70
-
-
60649089559
-
Highly sensitive feature detection for high resolution LC/MS
-
R. Tautenhahn, C. Bottcher, and S. Neumann Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics 9 2008 504
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 504
-
-
Tautenhahn, R.1
Bottcher, C.2
Neumann, S.3
-
71
-
-
33745228932
-
Multiscale processing of mass spectrometry data
-
DOI 10.1111/j.1541-0420.2005.00504.x
-
T.W. Randolph, and Y. Yasui Multiscale processing of mass spectrometry data Biometrics 62 2006 589 597 (Pubitemid 43926665)
-
(2006)
Biometrics
, vol.62
, Issue.2
, pp. 589-597
-
-
Randolph, T.W.1
Yasui, Y.2
-
72
-
-
58149209843
-
Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions
-
M.W. Senko, S.C. Beu, and F.W. Mclafferty Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions J. Am. Soc. Mass Spectrom. 6 1995 229 233
-
(1995)
J. Am. Soc. Mass Spectrom.
, vol.6
, pp. 229-233
-
-
Senko, M.W.1
Beu, S.C.2
McLafferty, F.W.3
-
73
-
-
67650733220
-
Highly accelerated feature detection in proteomics data sets using modern graphics processing units
-
R. Hussong, B. Gregorius, A. Tholey, and A. Hildebrandt Highly accelerated feature detection in proteomics data sets using modern graphics processing units Bioinformatics 25 2009 1937 1943
-
(2009)
Bioinformatics
, vol.25
, pp. 1937-1943
-
-
Hussong, R.1
Gregorius, B.2
Tholey, A.3
Hildebrandt, A.4
-
74
-
-
77951919202
-
Improved label-free LC-MS analysis by wavelet-based noise rejection
-
S. Cappadona, P. Nanni, M. Benevento, F. Levander, P. Versura, A. Roda, S. Cerutti, and L. Pattini Improved label-free LC-MS analysis by wavelet-based noise rejection J. Biomed. Biotechnol. 2010 2010 131505
-
(2010)
J. Biomed. Biotechnol.
, vol.2010
, pp. 131505
-
-
Cappadona, S.1
Nanni, P.2
Benevento, M.3
Levander, F.4
Versura, P.5
Roda, A.6
Cerutti, S.7
Pattini, L.8
-
75
-
-
46849101222
-
Wavelet-based method for noise characterization and rejection in high-performance liquid chromatography coupled to mass spectrometry
-
DOI 10.1021/ac800166w
-
S. Cappadona, F. Levander, M. Jansson, P. James, S. Cerutti, and L. Pattini Wavelet-based method for noise characterization and rejection in high-performance liquid chromatography coupled to mass spectrometry Anal. Chem. 80 2008 4960 4968 (Pubitemid 351956303)
-
(2008)
Analytical Chemistry
, vol.80
, Issue.13
, pp. 4960-4968
-
-
Cappadona, S.1
Levander, F.2
Jansson, M.3
James, P.4
Cerutti, S.5
Pattini, L.6
-
76
-
-
38149024942
-
Post alignment clustering procedure for comparative quantitative proteomics LC-MS data
-
J.C. de Groot, M.W. Fiers, R.C. van Ham, and A.H. America Post alignment clustering procedure for comparative quantitative proteomics LC-MS data Proteomics 8 2008 32 36
-
(2008)
Proteomics
, vol.8
, pp. 32-36
-
-
De Groot, J.C.1
Fiers, M.W.2
Van Ham, R.C.3
America, A.H.4
-
77
-
-
84857938446
-
Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins
-
(M111 014050)
-
T. Geiger, A. Wehner, C. Schaab, J. Cox, and M. Mann Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins Mol. Cell. Proteomics 11 2012 11 (M111 014050)
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 11
-
-
Geiger, T.1
Wehner, A.2
Schaab, C.3
Cox, J.4
Mann, M.5
-
78
-
-
0000857494
-
An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database
-
J.K. Eng, A.L. Mccormack, and J.R. Yates An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database J. Am. Soc. Mass Spectrom. 5 1994 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
-
79
-
-
38649083118
-
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
-
DOI 10.1021/pr700600n
-
L. Kall, J.D. Storey, M.J. MacCoss, and W.S. Noble Assigning significance to peptides identified by tandem mass spectrometry using decoy databases J. Proteome Res. 7 2008 29 34 (Pubitemid 351171110)
-
(2008)
Journal of Proteome Research
, vol.7
, Issue.1
, pp. 29-34
-
-
Kall, L.1
Storey, J.D.2
MacCoss, M.J.3
Noble, W.S.4
-
80
-
-
33947434519
-
Automated reporting from gel-based proteomics experiments using the open source Proteios database application
-
DOI 10.1002/pmic.200600814
-
F. Levander, M. Krogh, K. Warell, P. Garden, P. James, and J. Hakkinen Automated reporting from gel-based proteomics experiments using the open source Proteios database application Proteomics 7 2007 668 674 (Pubitemid 46450645)
-
(2007)
Proteomics
, vol.7
, Issue.5
, pp. 668-674
-
-
Levander, F.1
Krogh, M.2
Warell, K.3
Garden, P.4
James, P.5
Hakkinen, J.6
-
81
-
-
80053387432
-
IProphet: Multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
-
(M111 007690)
-
D. Shteynberg, E.W. Deutsch, H. Lam, J.K. Eng, Z. Sun, N. Tasman, L. Mendoza, R.L. Moritz, R. Aebersold, and A.I. Nesvizhskii iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates Mol. Cell. Proteomics 10 2011 (M111 007690)
-
(2011)
Mol. Cell. Proteomics
, vol.10
-
-
Shteynberg, D.1
Deutsch, E.W.2
Lam, H.3
Eng, J.K.4
Sun, Z.5
Tasman, N.6
Mendoza, L.7
Moritz, R.L.8
Aebersold, R.9
Nesvizhskii, A.I.10
-
82
-
-
63049120021
-
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
-
A.R. Jones, J.A. Siepen, S.J. Hubbard, and N.W. Paton Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines Proteomics 9 2009 1220 1229
-
(2009)
Proteomics
, vol.9
, pp. 1220-1229
-
-
Jones, A.R.1
Siepen, J.A.2
Hubbard, S.J.3
Paton, N.W.4
-
83
-
-
79959942025
-
MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines
-
T. Kwon, H. Choi, C. Vogel, A.I. Nesvizhskii, and E.M. Marcotte MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines J. Proteome Res. 10 2011 2949 2958
-
(2011)
J. Proteome Res.
, vol.10
, pp. 2949-2958
-
-
Kwon, T.1
Choi, H.2
Vogel, C.3
Nesvizhskii, A.I.4
Marcotte, E.M.5
-
84
-
-
77949768663
-
Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines
-
W. Yu, J.A. Taylor, M.T. Davis, L.E. Bonilla, K.A. Lee, P.L. Auger, C.C. Farnsworth, A.A. Welcher, and S.D. Patterson Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines Proteomics 10 2010 1172 1189
-
(2010)
Proteomics
, vol.10
, pp. 1172-1189
-
-
Yu, W.1
Taylor, J.A.2
Davis, M.T.3
Bonilla, L.E.4
Lee, K.A.5
Auger, P.L.6
Farnsworth, C.C.7
Welcher, A.A.8
Patterson, S.D.9
-
85
-
-
0042887140
-
Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry
-
DOI 10.1016/S1044-0305(03)00146-6
-
E.F. Strittmatter, P.L. Ferguson, K. Tang, and R.D. Smith Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry J. Am. Soc. Mass Spectrom. 14 2003 980 991 (Pubitemid 37040759)
-
(2003)
Journal of the American Society for Mass Spectrometry
, vol.14
, Issue.9
, pp. 980-991
-
-
Strittmatter, E.F.1
Ferguson, P.L.2
Tang, K.3
Smith, R.D.4
-
86
-
-
34547156610
-
A platform for accurate mass and time analyses of mass spectrometry data
-
DOI 10.1021/pr070146y
-
D. May, M. Fitzgibbon, Y. Liu, T. Holzman, J. Eng, C.J. Kemp, J. Whiteaker, A. Paulovich, and M. McIntosh A platform for accurate mass and time analyses of mass spectrometry data J. Proteome Res. 6 2007 2685 2694 (Pubitemid 47122364)
-
(2007)
Journal of Proteome Research
, vol.6
, Issue.7
, pp. 2685-2694
-
-
May, D.1
Fitzgibbon, M.2
Liu, Y.3
Holzman, T.4
Eng, J.5
Kemp, C.J.6
Whiteaker, J.7
Paulovich, A.8
McIntosh, M.9
-
87
-
-
61349134858
-
Peptide sequence confidence in accurate mass and time analysis and its use in complex proteomics experiments
-
D. May, Y. Liu, W. Law, M. Fitzgibbon, H. Wang, S. Hanash, and M. McIntosh Peptide sequence confidence in accurate mass and time analysis and its use in complex proteomics experiments J. Proteome Res. 7 2008 5148 5156
-
(2008)
J. Proteome Res.
, vol.7
, pp. 5148-5156
-
-
May, D.1
Liu, Y.2
Law, W.3
Fitzgibbon, M.4
Wang, H.5
Hanash, S.6
McIntosh, M.7
-
88
-
-
62549154087
-
Retention time alignment algorithms for LC/MS data must consider non-linear shifts
-
K. Podwojski, A. Fritsch, D.C. Chamrad, W. Paul, B. Sitek, K. Stuhler, P. Mutzel, C. Stephan, H.E. Meyer, W. Urfer, K. Ickstadt, and J. Rahnenfuhrer Retention time alignment algorithms for LC/MS data must consider non-linear shifts Bioinformatics 25 2009 758 764
-
(2009)
Bioinformatics
, vol.25
, pp. 758-764
-
-
Podwojski, K.1
Fritsch, A.2
Chamrad, D.C.3
Paul, W.4
Sitek, B.5
Stuhler, K.6
Mutzel, P.7
Stephan, C.8
Meyer, H.E.9
Urfer, W.10
Ickstadt, K.11
Rahnenfuhrer, J.12
-
89
-
-
80052674536
-
Software lock mass by two-dimensional minimization of peptide mass errors
-
J. Cox, A. Michalski, and M. Mann Software lock mass by two-dimensional minimization of peptide mass errors J. Am. Soc. Mass Spectrom. 22 2011 1373 1380
-
(2011)
J. Am. Soc. Mass Spectrom.
, vol.22
, pp. 1373-1380
-
-
Cox, J.1
Michalski, A.2
Mann, M.3
-
90
-
-
84877610614
-
An adaptive alignment algorithm for quality-controlled label-free LC-MS
-
M. Sandin, A. Ali, K. Hansson, O. Mansson, E. Andreasson, S. Resjo, and F. Levander An adaptive alignment algorithm for quality-controlled label-free LC-MS Mol. Cell. Proteomics 2013
-
(2013)
Mol. Cell. Proteomics
-
-
Sandin, M.1
Ali, A.2
Hansson, K.3
Mansson, O.4
Andreasson, E.5
Resjo, S.6
Levander, F.7
-
91
-
-
79952703214
-
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry
-
M.Y. Brusniak, S.T. Kwok, M. Christiansen, D. Campbell, L. Reiter, P. Picotti, U. Kusebauch, H. Ramos, E.W. Deutsch, J. Chen, R.L. Moritz, and R. Aebersold ATAQS: a computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry BMC Bioinformatics 12 2011 78
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 78
-
-
Brusniak, M.Y.1
Kwok, S.T.2
Christiansen, M.3
Campbell, D.4
Reiter, L.5
Picotti, P.6
Kusebauch, U.7
Ramos, H.8
Deutsch, E.W.9
Chen, J.10
Moritz, R.L.11
Aebersold, R.12
-
92
-
-
70349972789
-
MaRiMba: A software application for spectral library-based MRM transition list assembly
-
C.A. Sherwood, A. Eastham, L.W. Lee, A. Peterson, J.K. Eng, D. Shteynberg, L. Mendoza, E.W. Deutsch, J. Risler, N. Tasman, R. Aebersold, H. Lam, and D.B. Martin MaRiMba: a software application for spectral library-based MRM transition list assembly J. Proteome Res. 8 2009 4396 4405
-
(2009)
J. Proteome Res.
, vol.8
, pp. 4396-4405
-
-
Sherwood, C.A.1
Eastham, A.2
Lee, L.W.3
Peterson, A.4
Eng, J.K.5
Shteynberg, D.6
Mendoza, L.7
Deutsch, E.W.8
Risler, J.9
Tasman, N.10
Aebersold, R.11
Lam, H.12
Martin, D.B.13
-
94
-
-
43049090085
-
Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring
-
V. Lange, J.A. Malmstrom, J. Didion, N.L. King, B.P. Johansson, J. Schafer, J. Rameseder, C.H. Wong, E.W. Deutsch, M.Y. Brusniak, P. Buhlmann, L. Bjorck, B. Domon, and R. Aebersold Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring Mol. Cell. Proteomics 7 2008 1489 1500
-
(2008)
Mol. Cell. Proteomics
, vol.7
, pp. 1489-1500
-
-
Lange, V.1
Malmstrom, J.A.2
Didion, J.3
King, N.L.4
Johansson, B.P.5
Schafer, J.6
Rameseder, J.7
Wong, C.H.8
Deutsch, E.W.9
Brusniak, M.Y.10
Buhlmann, P.11
Bjorck, L.12
Domon, B.13
Aebersold, R.14
-
95
-
-
77951965920
-
Skyline: An open source document editor for creating and analyzing targeted proteomics experiments
-
B. MacLean, D.M. Tomazela, N. Shulman, M. Chambers, G.L. Finney, B. Frewen, R. Kern, D.L. Tabb, D.C. Liebler, and M.J. MacCoss Skyline: an open source document editor for creating and analyzing targeted proteomics experiments Bioinformatics 26 2010 966 968
-
(2010)
Bioinformatics
, vol.26
, pp. 966-968
-
-
Maclean, B.1
Tomazela, D.M.2
Shulman, N.3
Chambers, M.4
Finney, G.L.5
Frewen, B.6
Kern, R.7
Tabb, D.L.8
Liebler, D.C.9
Maccoss, M.J.10
-
96
-
-
82355184661
-
SRMBuilder: A user-friendly tool for selected reaction monitoring data analysis
-
Q. Sheng, C. Wu, Z. Su, and R. Zeng SRMBuilder: a user-friendly tool for selected reaction monitoring data analysis J. Bioinform. Comput. Biol. 9 Suppl. 1 2011 51 62
-
(2011)
J. Bioinform. Comput. Biol.
, vol.9
, Issue.SUPPL. 1
, pp. 51-62
-
-
Sheng, Q.1
Wu, C.2
Su, Z.3
Zeng, R.4
-
97
-
-
77949695871
-
Free computational resources for designing selected reaction monitoring transitions
-
J.A. Cham Mead, L. Bianco, and C. Bessant Free computational resources for designing selected reaction monitoring transitions Proteomics 10 2010 1106 1126
-
(2010)
Proteomics
, vol.10
, pp. 1106-1126
-
-
Cham Mead, J.A.1
Bianco, L.2
Bessant, C.3
-
98
-
-
84860862170
-
An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology
-
M.Y. Brusniak, C.S. Chu, U. Kusebauch, M.J. Sartain, J.D. Watts, and R.L. Moritz An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology Proteomics 12 2012 1176 1184
-
(2012)
Proteomics
, vol.12
, pp. 1176-1184
-
-
Brusniak, M.Y.1
Chu, C.S.2
Kusebauch, U.3
Sartain, M.J.4
Watts, J.D.5
Moritz, R.L.6
-
99
-
-
84866127272
-
Bioinformatic challenges in targeted proteomics
-
D. Reker, and L. Malmstrom Bioinformatic challenges in targeted proteomics J. Proteome Res. 2012
-
(2012)
J. Proteome Res.
-
-
Reker, D.1
Malmstrom, L.2
-
100
-
-
54049095667
-
A database of mass spectrometric assays for the yeast proteome
-
P. Picotti, H. Lam, D. Campbell, E.W. Deutsch, H. Mirzaei, J. Ranish, B. Domon, and R. Aebersold A database of mass spectrometric assays for the yeast proteome Nat. Methods 5 2008 913 914
-
(2008)
Nat. Methods
, vol.5
, pp. 913-914
-
-
Picotti, P.1
Lam, H.2
Campbell, D.3
Deutsch, E.W.4
Mirzaei, H.5
Ranish, J.6
Domon, B.7
Aebersold, R.8
-
101
-
-
84860856503
-
PASSEL: The PeptideAtlas SRMexperiment library
-
T. Farrah, E.W. Deutsch, R. Kreisberg, Z. Sun, D.S. Campbell, L. Mendoza, U. Kusebauch, M.Y. Brusniak, R. Huttenhain, R. Schiess, N. Selevsek, R. Aebersold, and R.L. Moritz PASSEL: the PeptideAtlas SRMexperiment library Proteomics 12 2012 1170 1175
-
(2012)
Proteomics
, vol.12
, pp. 1170-1175
-
-
Farrah, T.1
Deutsch, E.W.2
Kreisberg, R.3
Sun, Z.4
Campbell, D.S.5
Mendoza, L.6
Kusebauch, U.7
Brusniak, M.Y.8
Huttenhain, R.9
Schiess, R.10
Selevsek, N.11
Aebersold, R.12
Moritz, R.L.13
-
102
-
-
57049144338
-
MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments
-
D.B. Martin, T. Holzman, D. May, A. Peterson, A. Eastham, J. Eng, and M. McIntosh MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments Mol. Cell. Proteomics 7 2008 2270 2278
-
(2008)
Mol. Cell. Proteomics
, vol.7
, pp. 2270-2278
-
-
Martin, D.B.1
Holzman, T.2
May, D.3
Peterson, A.4
Eastham, A.5
Eng, J.6
McIntosh, M.7
-
103
-
-
75749126208
-
Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry
-
S.E. Abbatiello, D.R. Mani, H. Keshishian, and S.A. Carr Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry Clin. Chem. 56 2010 291 305
-
(2010)
Clin. Chem.
, vol.56
, pp. 291-305
-
-
Abbatiello, S.E.1
Mani, D.R.2
Keshishian, H.3
Carr, S.A.4
-
104
-
-
79955595074
-
MProphet: Automated data processing and statistical validation for large-scale SRM experiments
-
L. Reiter, O. Rinner, P. Picotti, R. Huttenhain, M. Beck, M.Y. Brusniak, M.O. Hengartner, and R. Aebersold mProphet: automated data processing and statistical validation for large-scale SRM experiments Nat. Methods 8 2011 430 435
-
(2011)
Nat. Methods
, vol.8
, pp. 430-435
-
-
Reiter, L.1
Rinner, O.2
Picotti, P.3
Huttenhain, R.4
Beck, M.5
Brusniak, M.Y.6
Hengartner, M.O.7
Aebersold, R.8
-
105
-
-
84857881072
-
Automated workflow for large-scale selected reaction monitoring experiments
-
L. Malmstrom, J. Malmstrom, N. Selevsek, G. Rosenberger, and R. Aebersold Automated workflow for large-scale selected reaction monitoring experiments J. Proteome Res. 11 2012 1644 1653
-
(2012)
J. Proteome Res.
, vol.11
, pp. 1644-1653
-
-
Malmstrom, L.1
Malmstrom, J.2
Selevsek, N.3
Rosenberger, G.4
Aebersold, R.5
-
106
-
-
84863624355
-
Automated selected reaction monitoring software for accurate label-free protein quantification
-
J. Teleman, C. Karlsson, S. Waldemarson, K. Hansson, P. James, J. Malmstrom, and F. Levander Automated selected reaction monitoring software for accurate label-free protein quantification J. Proteome Res. 11 2012 3766 3773
-
(2012)
J. Proteome Res.
, vol.11
, pp. 3766-3773
-
-
Teleman, J.1
Karlsson, C.2
Waldemarson, S.3
Hansson, K.4
James, P.5
Malmstrom, J.6
Levander, F.7
-
107
-
-
84860856325
-
Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate
-
H.A. Ebhardt, E. Sabido, R. Huttenhain, B. Collins, and R. Aebersold Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate Proteomics 12 2012 1185 1193
-
(2012)
Proteomics
, vol.12
, pp. 1185-1193
-
-
Ebhardt, H.A.1
Sabido, E.2
Huttenhain, R.3
Collins, B.4
Aebersold, R.5
-
108
-
-
79251595677
-
Data processing pipelines for comprehensive profiling of proteomics samples by label-free LC-MS for biomarker discovery
-
C. Christin, R. Bischoff, and P. Horvatovich Data processing pipelines for comprehensive profiling of proteomics samples by label-free LC-MS for biomarker discovery Talanta 83 2011 1209 1224
-
(2011)
Talanta
, vol.83
, pp. 1209-1224
-
-
Christin, C.1
Bischoff, R.2
Horvatovich, P.3
-
109
-
-
27644555055
-
Interpretation of shotgun proteomic data: The protein inference problem
-
DOI 10.1074/mcp.R500012-MCP200
-
A.I. Nesvizhskii, and R. Aebersold Interpretation of shotgun proteomic data: the protein inference problem Mol. Cell. Proteomics 4 2005 1419 1440 (Pubitemid 41555469)
-
(2005)
Molecular and Cellular Proteomics
, vol.4
, Issue.10
, pp. 1419-1440
-
-
Nesvizhskii, A.I.1
Aebersold, R.2
-
110
-
-
84869211929
-
Inference and validation of protein identifications
-
M. Claassen Inference and validation of protein identifications Mol. Cell. Proteomics 2012
-
(2012)
Mol. Cell. Proteomics
-
-
Claassen, M.1
-
111
-
-
80054013297
-
Enhanced information output from shotgun proteomics data by protein quantification and peptide quality control (PQPQ)
-
(M111 010264)
-
J. Forshed, H.J. Johansson, M. Pernemalm, R.M. Branca, A. Sandberg, and J. Lehtio Enhanced information output from shotgun proteomics data by protein quantification and peptide quality control (PQPQ) Mol. Cell. Proteomics 10 2011 (M111 010264)
-
(2011)
Mol. Cell. Proteomics
, vol.10
-
-
Forshed, J.1
Johansson, H.J.2
Pernemalm, M.3
Branca, R.M.4
Sandberg, A.5
Lehtio, J.6
-
112
-
-
70449433751
-
Protein quantification in label-free LC-MS experiments
-
T. Clough, M. Key, I. Ott, S. Ragg, G. Schadow, and O. Vitek Protein quantification in label-free LC-MS experiments J. Proteome Res. 8 2009 5275 5284
-
(2009)
J. Proteome Res.
, vol.8
, pp. 5275-5284
-
-
Clough, T.1
Key, M.2
Ott, I.3
Ragg, S.4
Schadow, G.5
Vitek, O.6
-
113
-
-
84859880168
-
Protein significance analysis in selected reaction monitoring (SRM) measurements
-
(M111 014662)
-
C.Y. Chang, P. Picotti, R. Huttenhain, V. Heinzelmann-Schwarz, M. Jovanovic, R. Aebersold, and O. Vitek Protein significance analysis in selected reaction monitoring (SRM) measurements Mol. Cell. Proteomics 11 2012 (M111 014662)
-
(2012)
Mol. Cell. Proteomics
, vol.11
-
-
Chang, C.Y.1
Picotti, P.2
Huttenhain, R.3
Heinzelmann-Schwarz, V.4
Jovanovic, M.5
Aebersold, R.6
Vitek, O.7
-
114
-
-
79952310105
-
Statistical issues in quality control of proteomic analyses: Good experimental design and planning
-
D.A. Cairns Statistical issues in quality control of proteomic analyses: good experimental design and planning Proteomics 11 2011 1037 1048
-
(2011)
Proteomics
, vol.11
, pp. 1037-1048
-
-
Cairns, D.A.1
-
115
-
-
40549141833
-
Design and analysis issues in quantitative proteomics studies
-
DOI 10.1002/pmic.200700683
-
N.A. Karp, and K.S. Lilley Design and analysis issues in quantitative proteomics studies Proteomics 7 Suppl. 1 2007 42 50 (Pubitemid 351547769)
-
(2007)
Proteomics - Practical Proteomics
, vol.2
, Issue.1
, pp. 42-50
-
-
Karp, N.A.1
Lilley, K.S.2
-
116
-
-
71049194213
-
Development and evaluation of normalization methods for label-free relative quantification of endogenous peptides
-
K. Kultima, A. Nilsson, B. Scholz, U.L. Rossbach, M. Falth, and P.E. Andren Development and evaluation of normalization methods for label-free relative quantification of endogenous peptides Mol. Cell. Proteomics 8 2009 2285 2295
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 2285-2295
-
-
Kultima, K.1
Nilsson, A.2
Scholz, B.3
Rossbach, U.L.4
Falth, M.5
Andren, P.E.6
-
117
-
-
32344442813
-
Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics
-
DOI 10.1021/pr050300l
-
S.J. Callister, R.C. Barry, J.N. Adkins, E.T. Johnson, W.J. Qian, B.J. Webb-Robertson, R.D. Smith, and M.S. Lipton Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics J. Proteome Res. 5 2006 277 286 (Pubitemid 43222296)
-
(2006)
Journal of Proteome Research
, vol.5
, Issue.2
, pp. 277-286
-
-
Callister, S.J.1
Barry, R.C.2
Adkins, J.N.3
Johnson, E.T.4
Qian, W.-J.5
Webb-Robertson, B.J.M.6
Smith, R.D.7
Lipton, M.S.8
-
118
-
-
82955187002
-
A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors
-
B.J. Webb-Robertson, M.M. Matzke, J.M. Jacobs, J.G. Pounds, and K.M. Waters A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors Proteomics 11 2011 4736 4741
-
(2011)
Proteomics
, vol.11
, pp. 4736-4741
-
-
Webb-Robertson, B.J.1
Matzke, M.M.2
Jacobs, J.M.3
Pounds, J.G.4
Waters, K.M.5
-
119
-
-
0022186670
-
Measurement of protein using bicinchoninic acid
-
DOI 10.1016/0003-2697(85)90442-7
-
P.K. Smith, R.I. Krohn, G.T. Hermanson, A.K. Mallia, F.H. Gartner, M.D. Provenzano, E.K. Fujimoto, N.M. Goeke, B.J. Olson, and D.C. Klenk Measurement of protein using bicinchoninic acid Anal. Biochem. 150 1985 76 85 (Pubitemid 16258399)
-
(1985)
Analytical Biochemistry
, vol.150
, Issue.1
, pp. 76-85
-
-
Smith, P.K.1
Krohn, R.I.2
Hermanson, G.T.3
-
120
-
-
34548428842
-
The association of biomolecular resource facilities proteomics research group 2006 study: Relative protein quantitation
-
DOI 10.1074/mcp.M700165-MCP200
-
C.W. Turck, A.M. Falick, J.A. Kowalak, W.S. Lane, K.S. Lilley, B.S. Phinney, S.T. Weintraub, H.E. Witkowska, and N.A. Yates The Association of Biomolecular Resource Facilities Proteomics Research Group 2006 study: relative protein quantitation Mol. Cell. Proteomics 6 2007 1291 1298 (Pubitemid 47365429)
-
(2007)
Molecular and Cellular Proteomics
, vol.6
, Issue.8
, pp. 1291-1298
-
-
Turck, C.W.1
Falick, A.M.2
Kowalak, J.A.3
Lane, W.S.4
Lilley, K.S.5
Phinney, B.S.6
Weintraub, S.T.7
Witkowska, H.E.8
Yates, N.A.9
-
122
-
-
42049089764
-
Information quality in proteomics
-
DOI 10.1093/bib/bbn004, Computational Proteomics
-
D.A. Stead, N.W. Paton, P. Missier, S.M. Embury, C. Hedeler, B. Jin, A.J. Brown, and A. Preece Information quality in proteomics Brief. Bioinform. 9 2008 174 188 (Pubitemid 351517003)
-
(2008)
Briefings in Bioinformatics
, vol.9
, Issue.2
, pp. 174-188
-
-
Stead, D.A.1
Paton, N.W.2
Missier, P.3
Embury, S.M.4
Hedeler, C.5
Jin, B.6
Brown, A.J.P.7
Preece, A.8
-
123
-
-
67349196123
-
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
-
A.W. Bell, E.W. Deutsch, C.E. Au, R.E. Kearney, R. Beavis, S. Sechi, T. Nilsson, and J.J. Bergeron A HUPO test sample study reveals common problems in mass spectrometry-based proteomics Nat. Methods 6 2009 423 430
-
(2009)
Nat. Methods
, vol.6
, pp. 423-430
-
-
Bell, A.W.1
Deutsch, E.W.2
Au, C.E.3
Kearney, R.E.4
Beavis, R.5
Sechi, S.6
Nilsson, T.7
Bergeron, J.J.8
-
124
-
-
70349617072
-
Comparative analysis to guide quality improvements in proteomics
-
M. Mann Comparative analysis to guide quality improvements in proteomics Nat. Methods 6 2009 717 719
-
(2009)
Nat. Methods
, vol.6
, pp. 717-719
-
-
Mann, M.1
-
125
-
-
84859987789
-
A proteomics performance standard to support measurement quality in proteomics
-
A. Beasley-Green, D. Bunk, P. Rudnick, L. Kilpatrick, and K. Phinney A proteomics performance standard to support measurement quality in proteomics Proteomics 12 2012 923 931
-
(2012)
Proteomics
, vol.12
, pp. 923-931
-
-
Beasley-Green, A.1
Bunk, D.2
Rudnick, P.3
Kilpatrick, L.4
Phinney, K.5
-
126
-
-
76649122499
-
Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance
-
A.G. Paulovich, D. Billheimer, A.J. Ham, L. Vega-Montoto, P.A. Rudnick, D.L. Tabb, P. Wang, R.K. Blackman, D.M. Bunk, H.L. Cardasis, K.R. Clauser, C.R. Kinsinger, B. Schilling, T.J. Tegeler, A.M. Variyath, M. Wang, J.R. Whiteaker, L.J. Zimmerman, D. Fenyo, S.A. Carr, S.J. Fisher, B.W. Gibson, M. Mesri, T.A. Neubert, F.E. Regnier, H. Rodriguez, C. Spiegelman, S.E. Stein, P. Tempst, and D.C. Liebler Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance Mol. Cell. Proteomics 9 2010 242 254
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 242-254
-
-
Paulovich, A.G.1
Billheimer, D.2
Ham, A.J.3
Vega-Montoto, L.4
Rudnick, P.A.5
Tabb, D.L.6
Wang, P.7
Blackman, R.K.8
Bunk, D.M.9
Cardasis, H.L.10
Clauser, K.R.11
Kinsinger, C.R.12
Schilling, B.13
Tegeler, T.J.14
Variyath, A.M.15
Wang, M.16
Whiteaker, J.R.17
Zimmerman, L.J.18
Fenyo, D.19
Carr, S.A.20
Fisher, S.J.21
Gibson, B.W.22
Mesri, M.23
Neubert, T.A.24
Regnier, F.E.25
Rodriguez, H.26
Spiegelman, C.27
Stein, S.E.28
Tempst, P.29
Liebler, D.C.30
more..
-
127
-
-
79952285447
-
Simulating and validating proteomics data and search results
-
S.J. Geromanos, C. Hughes, D. Golick, S. Ciavarini, M.V. Gorenstein, K. Richardson, J.B. Hoyes, J.P. Vissers, and J.I. Langridge Simulating and validating proteomics data and search results Proteomics 11 2011 1189 1211
-
(2011)
Proteomics
, vol.11
, pp. 1189-1211
-
-
Geromanos, S.J.1
Hughes, C.2
Golick, D.3
Ciavarini, S.4
Gorenstein, M.V.5
Richardson, K.6
Hoyes, J.B.7
Vissers, J.P.8
Langridge, J.I.9
-
128
-
-
55349093999
-
LC-MSsim - A simulation software for liquid chromatography mass spectrometry data
-
O. Schulz-Trieglaff, N. Pfeifer, C. Gropl, O. Kohlbacher, and K. Reinert LC-MSsim - a simulation software for liquid chromatography mass spectrometry data BMC Bioinformatics 9 2008 423
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 423
-
-
Schulz-Trieglaff, O.1
Pfeifer, N.2
Gropl, C.3
Kohlbacher, O.4
Reinert, K.5
-
130
-
-
84863609997
-
TOPPAS: A graphical workflow editor for the analysis of high-throughput proteomics data
-
J. Junker, C. Bielow, A. Bertsch, M. Sturm, K. Reinert, and O. Kohlbacher TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data J. Proteome Res. 11 2012 3914 3920
-
(2012)
J. Proteome Res.
, vol.11
, pp. 3914-3920
-
-
Junker, J.1
Bielow, C.2
Bertsch, A.3
Sturm, M.4
Reinert, K.5
Kohlbacher, O.6
-
131
-
-
65549119729
-
Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments
-
O. Schulz-Trieglaff, E. Machtejevas, K. Reinert, H. Schluter, J. Thiemann, and K. Unger Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments BioData Min 2 2009 4
-
(2009)
BioData Min
, vol.2
, pp. 4
-
-
Schulz-Trieglaff, O.1
Machtejevas, E.2
Reinert, K.3
Schluter, H.4
Thiemann, J.5
Unger, K.6
-
132
-
-
54349106196
-
Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements
-
E. Lange, R. Tautenhahn, S. Neumann, and C. Gropl Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements BMC Bioinformatics 9 2008 375
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 375
-
-
Lange, E.1
Tautenhahn, R.2
Neumann, S.3
Gropl, C.4
-
133
-
-
33745828376
-
Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profiles
-
DOI 10.1021/pr050436j
-
B.D. Piening, P. Wang, C.S. Bangur, J. Whiteaker, H. Zhang, L.C. Feng, J.F. Keane, J.K. Eng, H. Tang, A. Prakash, M.W. McIntosh, and A. Paulovich Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profiles J. Proteome Res. 5 2006 1527 1534 (Pubitemid 44036126)
-
(2006)
Journal of Proteome Research
, vol.5
, Issue.7
, pp. 1527-1534
-
-
Piening, B.D.1
Wang, P.2
Bangur, C.S.3
Whiteaker, J.4
Zhang, H.5
Feng, L.-C.6
Keane, J.F.7
Eng, J.K.8
Tang, H.9
Prakash, A.10
McIntosh, M.W.11
Paulovich, A.12
-
134
-
-
78249241486
-
Evaluation for computational platforms of LC-MS based label-free quantitative proteomics: A global view
-
R. Zhang, A. Barton, J. Brittenden, J. Huang, and D. Crowther Evaluation for computational platforms of LC-MS based label-free quantitative proteomics: a global view Journal of Proteomics & Bioinformatics 3 2010 260 265
-
(2010)
Journal of Proteomics & Bioinformatics
, vol.3
, pp. 260-265
-
-
Zhang, R.1
Barton, A.2
Brittenden, J.3
Huang, J.4
Crowther, D.5
-
135
-
-
78449311334
-
Evaluation of peak picking quality in LC-MS metabolomics data
-
L. Brodsky, A. Moussaieff, N. Shahaf, A. Aharoni, and I. Rogachev Evaluation of peak picking quality in LC-MS metabolomics data Anal. Chem. 82 2010 9177 9187
-
(2010)
Anal. Chem.
, vol.82
, pp. 9177-9187
-
-
Brodsky, L.1
Moussaieff, A.2
Shahaf, N.3
Aharoni, A.4
Rogachev, I.5
-
136
-
-
84864625050
-
Strategy for optimizing LC-MS data processing in metabolomics: A design of experiments approach
-
M. Eliasson, S. Rannar, R. Madsen, M.A. Donten, E. Marsden-Edwards, T. Moritz, J.P. Shockcor, E. Johansson, and J. Trygg Strategy for optimizing LC-MS data processing in metabolomics: a design of experiments approach Anal. Chem. 84 2012 6869 6876
-
(2012)
Anal. Chem.
, vol.84
, pp. 6869-6876
-
-
Eliasson, M.1
Rannar, S.2
Madsen, R.3
Donten, M.A.4
Marsden-Edwards, E.5
Moritz, T.6
Shockcor, J.P.7
Johansson, E.8
Trygg, J.9
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