-
1
-
-
77956304093
-
Mass spectrometry in high-throughput proteomics: ready for the big time
-
Nilsson, T., Mann, M., Aebersold, R., Yates, J. R., 3rd et al., 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 3rd, J.R.4
-
2
-
-
34047109196
-
Methods for samples preparation in proteomic research
-
Bodzon-Kulakowska, A., Bierczynska-Krzysik, A., Dylag, T., Drabik, A. et al., Methods for samples preparation in proteomic research. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2007, 849, 1-31.
-
(2007)
J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.
, vol.849
, pp. 1-31
-
-
Bodzon-Kulakowska, A.1
Bierczynska-Krzysik, A.2
Dylag, T.3
Drabik, A.4
-
3
-
-
34248598796
-
Trends in sample preparation for classical and second generation proteomics
-
Canas, B., Pineiro, C., Calvo, E., Lopez-Ferrer, D., Gallardo, J. M., Trends in sample preparation for classical and second generation proteomics. J. Chromatogr. A 2007, 1153, 235-258.
-
(2007)
J. Chromatogr. A
, vol.1153
, pp. 235-258
-
-
Canas, B.1
Pineiro, C.2
Calvo, E.3
Lopez-Ferrer, D.4
Gallardo, J.M.5
-
4
-
-
34748910605
-
Sample preparation by in-gel digestion for mass spectrometry-based proteomics
-
Granvogl, B., Ploscher, M., Eichacker, L. A., Sample preparation by in-gel digestion for mass spectrometry-based proteomics. Anal. Bioanal. Chem. 2007, 389, 991-1002.
-
(2007)
Anal. Bioanal. Chem.
, vol.389
, pp. 991-1002
-
-
Granvogl, B.1
Ploscher, M.2
Eichacker, L.A.3
-
5
-
-
84855877960
-
Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics
-
Burkhart, J. M., Schumbrutzki, C., Wortelkamp, S., Sickmann, A., Zahedi, R. P., Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics. J. Proteomics 2012, 75, 1454-62.
-
(2012)
J. Proteomics
, vol.75
, pp. 1454-1462
-
-
Burkhart, J.M.1
Schumbrutzki, C.2
Wortelkamp, S.3
Sickmann, A.4
Zahedi, R.P.5
-
6
-
-
34548400394
-
A la carte proteomics with an emphasis on gel-free techniques
-
Gevaert, K., Van Damme, P., Ghesquiere, B., Impens, F. et al., A la carte proteomics with an emphasis on gel-free techniques. Proteomics 2007, 7, 2698-2718.
-
(2007)
Proteomics
, vol.7
, pp. 2698-2718
-
-
Gevaert, K.1
Van Damme, P.2
Ghesquiere, B.3
Impens, F.4
-
7
-
-
0024438708
-
Electrospray ionization for mass spectrometry of large biomolecules
-
Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., Whitehouse, C. M., Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246, 64-71.
-
(1989)
Science
, vol.246
, pp. 64-71
-
-
Fenn, J.B.1
Mann, M.2
Meng, C.K.3
Wong, S.F.4
Whitehouse, C.M.5
-
8
-
-
84875463071
-
Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers
-
Hillenkamp, F., Karas, M., Beavis, R. C., Chait, B. T., Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Anal. Chem. 1991, 63, 1193A-1203A.
-
(1991)
Anal. Chem.
, vol.63
-
-
Hillenkamp, F.1
Karas, M.2
Beavis, R.C.3
Chait, B.T.4
-
9
-
-
79952303580
-
A global analysis of peptide fragmentation variability
-
Barsnes, H., Eidhammer, I., Martens, L., A global analysis of peptide fragmentation variability. Proteomics 2011, 11, 1181-1188.
-
(2011)
Proteomics
, vol.11
, pp. 1181-1188
-
-
Barsnes, H.1
Eidhammer, I.2
Martens, L.3
-
10
-
-
0041408938
-
Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis
-
Makarov, A., Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Anal. Chem. 2000, 72, 1156-1162.
-
(2000)
Anal. Chem.
, vol.72
, pp. 1156-1162
-
-
Makarov, A.1
-
11
-
-
77957221582
-
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
-
Nesvizhskii, A. I., A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J. Proteomics 2010, 73, 2092-2123.
-
(2010)
J. Proteomics
, vol.73
, pp. 2092-2123
-
-
Nesvizhskii, A.I.1
-
12
-
-
84876692278
-
Crowdsourcing in proteomics: public resources lead to better experiments
-
Barsnes, H., Martens, L., Crowdsourcing in proteomics: public resources lead to better experiments. Amino Acids 2013, 44, 1129-1137.
-
(2013)
Amino Acids
, vol.44
, pp. 1129-1137
-
-
Barsnes, H.1
Martens, L.2
-
13
-
-
84870596405
-
Current methods for global proteome identification
-
Vaudel, M., Sickmann, A., Martens, L., Current methods for global proteome identification. Expert Rev. Proteomics 2012, 9, 519-532.
-
(2012)
Expert Rev. Proteomics
, vol.9
, pp. 519-532
-
-
Vaudel, M.1
Sickmann, A.2
Martens, L.3
-
14
-
-
34547176285
-
Proteomics data validation: why all must provide data
-
Martens, L., Hermjakob, H., Proteomics data validation: why all must provide data. Mol. Biosyst. 2007, 3, 518-522.
-
(2007)
Mol. Biosyst.
, vol.3
, pp. 518-522
-
-
Martens, L.1
Hermjakob, H.2
-
15
-
-
84890548691
-
Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics
-
Vaudel, M., Sickmann, A., Martens, L., Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics. Biochim. Biophys. Acta 2014, 1844, 12-20.
-
(2014)
Biochim. Biophys. Acta
, vol.1844
, pp. 12-20
-
-
Vaudel, M.1
Sickmann, A.2
Martens, L.3
-
16
-
-
76149098839
-
Unbiased statistical analysis for multi-stage proteomic search strategies
-
Everett, L. J., Bierl, C., Master, S. R., Unbiased statistical analysis for multi-stage proteomic search strategies. J. Proteome Res. 2010, 9, 700-707.
-
(2010)
J. Proteome Res.
, vol.9
, pp. 700-707
-
-
Everett, L.J.1
Bierl, C.2
Master, S.R.3
-
17
-
-
79953170260
-
Interpretation of data underlying the link between colony collapse disorder (CCD) and an invertebrate iridescent virus
-
Foster, L. J., Interpretation of data underlying the link between colony collapse disorder (CCD) and an invertebrate iridescent virus. Mol. Cell Proteomics 2011, 10, M110.006387.
-
(2011)
Mol. Cell Proteomics
, vol.10
-
-
Foster, L.J.1
-
18
-
-
84883355771
-
Matters of significance
-
Editors
-
Editors, Matters of significance. Nat. Methods 2013, 10, 805.
-
(2013)
Nat. Methods
, vol.10
, pp. 805
-
-
-
19
-
-
84893351260
-
PROTEINCHALLENGE: crowd sourcing in proteomics analysis and software development
-
Martin, S. F., Falkenberg, H., Dyrlund, T. F., Khoudoli, G. A. et al., PROTEINCHALLENGE: crowd sourcing in proteomics analysis and software development. J. Proteomics 2013, 88, 41-46.
-
(2013)
J. Proteomics
, vol.88
, pp. 41-46
-
-
Martin, S.F.1
Falkenberg, H.2
Dyrlund, T.F.3
Khoudoli, G.A.4
-
20
-
-
84885582360
-
In need of an upgrade
-
Editors
-
Editors, In need of an upgrade. Nat. Biotechnol. 2013, 31, 857.
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 857
-
-
-
21
-
-
84863012827
-
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles)
-
Kinsinger, C. R., Apffel, J., Baker, M., Bian, X. et al., Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). J. Proteome Res. 2012, 11, 1412-1419.
-
(2012)
J. Proteome Res.
, vol.11
, pp. 1412-1419
-
-
Kinsinger, C.R.1
Apffel, J.2
Baker, M.3
Bian, X.4
-
22
-
-
79952294100
-
Quality control in proteomics
-
Martens, L., Vizcaino, J. A., Banks, R., Quality control in proteomics. Proteomics 2011, 11, 1015-1016.
-
(2011)
Proteomics
, vol.11
, pp. 1015-1016
-
-
Martens, L.1
Vizcaino, J.A.2
Banks, R.3
-
23
-
-
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. et al., SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments. J. Proteome Res. 2012, 11, 5540-5547.
-
(2012)
J. Proteome Res.
, vol.11
, pp. 5540-5547
-
-
Pichler, P.1
Mazanek, M.2
Dusberger, F.3
Weilnbock, L.4
-
24
-
-
54049090766
-
Selected reaction monitoring for quantitative proteomics: a tutorial
-
Lange, V., Picotti, P., Domon, B., Aebersold, R., Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol. 2008, 4, 222.
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 222
-
-
Lange, V.1
Picotti, P.2
Domon, B.3
Aebersold, R.4
-
25
-
-
38549097071
-
The universal protein resource (UniProt)
-
UniProt Consortium
-
UniProt Consortium, The universal protein resource (UniProt). Nucleic Acids Res. 2008, 36, D190-D195.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
-
26
-
-
84867345063
-
A cross-platform toolkit for mass spectrometry and proteomics
-
Chambers, M. C., Maclean, B., Burke, R., Amodei, D. et al., A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 2012, 30, 918-920.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 918-920
-
-
Chambers, M.C.1
Maclean, B.2
Burke, R.3
Amodei, D.4
-
27
-
-
7044246160
-
Open mass spectrometry search algorithm
-
Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L. et al., Open mass spectrometry search algorithm. J. Proteome Res. 2004, 3, 958-964.
-
(2004)
J. Proteome Res.
, vol.3
, pp. 958-964
-
-
Geer, L.Y.1
Markey, S.P.2
Kowalak, J.A.3
Wagner, L.4
-
28
-
-
0037442649
-
A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
-
Fenyo, D., Beavis, R. C., A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem. 2003, 75, 768-774.
-
(2003)
Anal. Chem.
, vol.75
, pp. 768-774
-
-
Fenyo, D.1
Beavis, R.C.2
-
29
-
-
79951750784
-
SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches
-
Vaudel, M., Barsnes, H., Berven, F. S., Sickmann, A., Martens, L., SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics 2011, 11, 996-999.
-
(2011)
Proteomics
, vol.11
, pp. 996-999
-
-
Vaudel, M.1
Barsnes, H.2
Berven, F.S.3
Sickmann, A.4
Martens, L.5
-
30
-
-
77449146854
-
Target-decoy search strategy for mass spectrometry-based proteomics
-
Elias, J. E., Gygi, S. P., Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol. Biol. 2010, 604, 55-71.
-
(2010)
Methods Mol. Biol.
, vol.604
, pp. 55-71
-
-
Elias, J.E.1
Gygi, S.P.2
-
31
-
-
84875391572
-
Ensembl 2013
-
Flicek, P., Ahmed, I., Amode, M. R., Barrell, D. et al., Ensembl 2013. Nucleic Acids Res. 2013, 41, D48-D55.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Flicek, P.1
Ahmed, I.2
Amode, M.R.3
Barrell, D.4
-
32
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D. et al., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25, 25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
-
33
-
-
80052780634
-
Dasty3, a WEB framework for DAS
-
Villaveces, J. M., Jimenez, R. C., Garcia, L. J., Salazar, G. A. et al., Dasty3, a WEB framework for DAS. Bioinformatics 2011, 27, 2616-2617.
-
(2011)
Bioinformatics
, vol.27
, pp. 2616-2617
-
-
Villaveces, J.M.1
Jimenez, R.C.2
Garcia, L.J.3
Salazar, G.A.4
-
34
-
-
84876515907
-
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
-
Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M. et al., STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013, 41, D808-D815.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Franceschini, A.1
Szklarczyk, D.2
Frankild, S.3
Kuhn, M.4
-
35
-
-
58149177166
-
Reactome knowledgebase of human biological pathways and processes
-
Matthews, L., Gopinath, G., Gillespie, M., Caudy, M. et al., Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 2009, 37, D619-D622.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Matthews, L.1
Gopinath, G.2
Gillespie, M.3
Caudy, M.4
-
36
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G. et al., The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
-
37
-
-
65549111862
-
Charting online OMICS resources: a navigational chart for clinical researchers
-
Vizcaino, J. A., Mueller, M., Hermjakob, H., Martens, L., Charting online OMICS resources: a navigational chart for clinical researchers. Proteomics Clin. Appl. 2009, 3, 18-29.
-
(2009)
Proteomics Clin. Appl.
, vol.3
, pp. 18-29
-
-
Vizcaino, J.A.1
Mueller, M.2
Hermjakob, H.3
Martens, L.4
-
38
-
-
23944526367
-
PRIDE: the proteomics identifications database
-
Martens, L., Hermjakob, H., Jones, P., Adamski, M. et al., PRIDE: the proteomics identifications database. Proteomics 2005, 5, 3537-3545.
-
(2005)
Proteomics
, vol.5
, pp. 3537-3545
-
-
Martens, L.1
Hermjakob, H.2
Jones, P.3
Adamski, M.4
-
39
-
-
84863011685
-
PRIDE Inspector: a tool to visualize and validate MS proteomics data
-
Wang, R., Fabregat, A., Rios, D., Ovelleiro, D. et al., PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nat. Biotechnol. 2012, 30, 135-137.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 135-137
-
-
Wang, R.1
Fabregat, A.2
Rios, D.3
Ovelleiro, D.4
|