-
1
-
-
18744384734
-
Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum
-
DOI 10.1093/bioinformatics/bti254
-
Morris, J. S.; Coombes, K. R.; Koomen, J.; Baggerly, K. A.; Kobayashi, R. Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum Bioinformatics 2005, 21, 1764-75 (Pubitemid 40674202)
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 1764-1775
-
-
Morris, J.S.1
Coombes, K.R.2
Koomen, J.3
Baggerly, K.A.4
Kobayashi, R.5
-
2
-
-
18744410496
-
Understanding the characteristics of mass spectrometry data through the use of simulation
-
Coombes, K. R.; Koomen, J. M.; Baggerly, K. A.; Morris, J. S.; Kobayashi, R. Understanding the characteristics of mass spectrometry data through the use of simulation Cancer Inform. 2005, 1, 41-52
-
(2005)
Cancer Inform.
, vol.1
, pp. 41-52
-
-
Coombes, K.R.1
Koomen, J.M.2
Baggerly, K.A.3
Morris, J.S.4
Kobayashi, R.5
-
3
-
-
55349093999
-
LC-MSsim-a simulation software for liquid chromatography mass spectrometry data
-
Schulz-Trieglaff, O.; Pfeifer, N.; Gröpl, C.; Kohlbacher, O.; Reinert, K. LC-MSsim-a simulation software for liquid chromatography mass spectrometry data BMC Bioinform. 2008, 9, 423
-
(2008)
BMC Bioinform.
, vol.9
, pp. 423
-
-
Schulz-Trieglaff, O.1
Pfeifer, N.2
Gröpl, C.3
Kohlbacher, O.4
Reinert, K.5
-
4
-
-
60649091300
-
NITPICK: Peak identification for mass spectrometry data
-
Renard, B. Y.; Kirchner, M.; Steen, H.; Steen, J. A. J.; Hamprecht, F. A. NITPICK: peak identification for mass spectrometry data BMC Bioinform. 2008, 9, 355
-
(2008)
BMC Bioinform.
, vol.9
, pp. 355
-
-
Renard, B.Y.1
Kirchner, M.2
Steen, H.3
Steen, J.A.J.4
Hamprecht, F.A.5
-
5
-
-
60549117342
-
Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis
-
Yang, C.; He, Z.; Yu, W. Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis BMC Bioinform. 2009, 10, 4
-
(2009)
BMC Bioinform.
, vol.10
, pp. 4
-
-
Yang, C.1
He, Z.2
Yu, W.3
-
6
-
-
42249108173
-
OpenMS - An open-source software framework for mass spectrometry
-
Sturm, M.; Bertsch, A.; Gröpl, C.; Hildebrandt, A.; Hussong, R.; Lange, E.; Pfeifer, N.; Schulz-Trieglaff, O.; Zerck, A.; Reinert, K.; Kohlbacher, O. OpenMS-an open-source software framework for mass spectrometry BMC Bioinform. 2008, 9, 163
-
(2008)
BMC Bioinform.
, vol.9
, pp. 163
-
-
Sturm, M.1
Bertsch, A.2
Gröpl, 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
-
7
-
-
33846706581
-
TOPP-the OpenMS proteomics pipeline
-
Kohlbacher, O.; Reinert, K.; Gröpl, C.; Lange, E.; Pfeifer, N.; Schulz-Trieglaff, O.; Sturm, M. TOPP-the OpenMS proteomics pipeline Bioinformatics 2007, 23, e191-7
-
(2007)
Bioinformatics
, vol.23
, pp. 191-7
-
-
Kohlbacher, O.1
Reinert, K.2
Gröpl, C.3
Lange, E.4
Pfeifer, N.5
Schulz-Trieglaff, O.6
Sturm, M.7
-
8
-
-
2942568222
-
Unimod: Protein modifications for mass spectrometry
-
DOI 10.1002/pmic.200300744
-
Creasy, D. M.; Cottrell, J. S. Unimod: Protein modifications for mass spectrometry Proteomics 2004, 4, 1534-6 (Pubitemid 38738312)
-
(2004)
Proteomics
, vol.4
, Issue.6
, pp. 1534-1536
-
-
Creasy, D.M.1
Cottrell, J.S.2
-
9
-
-
33846632267
-
Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics
-
DOI 10.1021/pr060507u
-
Siepen, J. A.; Keevil, E.-J.; Knight, D.; Hubbard, S. J. Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics J. Proteome Res. 2007, 6, 399-408 (Pubitemid 46173693)
-
(2007)
Journal of Proteome Research
, vol.6
, Issue.1
, pp. 399-408
-
-
Siepen, J.A.1
Keevil, E.-J.2
Knight, D.3
Hubbard, S.J.4
-
10
-
-
0026522221
-
Pharmaceutical Drug Separations by HPCE: Practical Guidelines
-
Laughlin, G. M. M.; Nolan, J. A.; Lindahl, J. L.; Palmieri, R. H.; Anderson, K. W.; Morris, S. C.; Morrison, J. A.; Bronzert, T. J. Pharmaceutical Drug Separations by HPCE: Practical Guidelines J. Liq. Chromatogr. Relat. Technol. 1992, 15, 961-1021
-
(1992)
J. Liq. Chromatogr. Relat. Technol.
, vol.15
, pp. 961-1021
-
-
Laughlin, G.M.M.1
Nolan, J.A.2
Lindahl, J.L.3
Palmieri, R.H.4
Anderson, K.W.5
Morris, S.C.6
Morrison, J.A.7
Bronzert, T.J.8
-
11
-
-
39849105680
-
Statistical learning of peptide retention behavior in chromatographic separations: A new kernel-based approach for computational proteomics
-
Pfeifer, N.; Leinenbach, A.; Huber, C. G.; Kohlbacher, O. Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics BMC Bioinform. 2007, 8, 468
-
(2007)
BMC Bioinform.
, vol.8
, pp. 468
-
-
Pfeifer, N.1
Leinenbach, A.2
Huber, C.G.3
Kohlbacher, O.4
-
12
-
-
0035957820
-
A hybrid of exponential and gaussian functions as a simple model of asymmetric chromatographic peaks
-
DOI 10.1016/S0021-9673(01)00594-5, PII S0021967301005945
-
Lan, K.; Jorgenson, J. W. A hybrid of exponential and gaussian functions as a simple model of asymmetric chromatographic peaks J. Chromatogr. A 2001, 915, 1-13 (Pubitemid 32289320)
-
(2001)
Journal of Chromatography A
, vol.915
, Issue.1-2
, pp. 1-13
-
-
Lan, K.1
Jorgenson, J.W.2
-
13
-
-
0025830123
-
Calculation of isotope distributions in mass spectrometry. A trivial solution for a non-trivial problem
-
Kubinyi, H. Calculation of isotope distributions in mass spectrometry. A trivial solution for a non-trivial problem Anal. Chim. Acta 1991, 247, 107-19
-
(1991)
Anal. Chim. Acta
, vol.247
, pp. 107-19
-
-
Kubinyi, H.1
-
15
-
-
33645654439
-
Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer
-
Makarov, A.; Denisov, E.; Kholomeev, A.; Balschun, W.; Lange, O.; Strupat, K.; Horning, S. Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer Anal. Chem. 2006, 78, 2113-20
-
(2006)
Anal. Chem.
, vol.78
, pp. 2113-20
-
-
Makarov, A.1
Denisov, E.2
Kholomeev, A.3
Balschun, W.4
Lange, O.5
Strupat, K.6
Horning, S.7
-
16
-
-
3242660851
-
Prediction of low-energy collision-induced dissociation spectra of peptides
-
DOI 10.1021/ac049951b
-
Zhang, Z. Prediction of low-energy collision-induced dissociation spectra of peptides Anal. Chem. 2004, 76, 3908-22 (Pubitemid 38943659)
-
(2004)
Analytical Chemistry
, vol.76
, Issue.14
, pp. 3908-3922
-
-
Zhang, Z.1
-
17
-
-
36348959863
-
A machine learning approach to predicting peptide fragmentation spectra
-
Arnold, R. J.; Jayasankar, N.; Aggarwal, D.; Tang, H.; Radivojac, P. A machine learning approach to predicting peptide fragmentation spectra Pacific Symp. Biocomput. 2006, 230, 219-30
-
(2006)
Pacific Symp. Biocomput.
, vol.230
, pp. 219-30
-
-
Arnold, R.J.1
Jayasankar, N.2
Aggarwal, D.3
Tang, H.4
Radivojac, P.5
-
18
-
-
51249111303
-
A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data
-
Zhou, C.; Bowler, L. D.; Feng, J. A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data BMC Bioinform. 2008, 9, 325
-
(2008)
BMC Bioinform.
, vol.9
, pp. 325
-
-
Zhou, C.1
Bowler, L.D.2
Feng, J.3
-
19
-
-
0742305695
-
Intensity-based protein identification by machine learning from a library of tandem mass spectra
-
DOI 10.1038/nbt930
-
Elias, J. E.; Gibbons, F. D.; King, O. D.; Roth, F. P.; Gygi, S. P. Intensity-based protein identification by machine learning from a library of tandem mass spectra Nat. Biotechnol. 2004, 22, 214-9 (Pubitemid 38160538)
-
(2004)
Nature Biotechnology
, vol.22
, Issue.2
, pp. 214-219
-
-
Elias, J.E.1
Gibbons, F.D.2
King, O.D.3
Roth, F.P.4
Gygi, S.P.5
-
20
-
-
66749169317
-
Predicting intensity ranks of peptide fragment ions
-
Frank, A. M. Predicting intensity ranks of peptide fragment ions J. Proteome Res. 2009, 8, 2226-40
-
(2009)
J. Proteome Res.
, vol.8
, pp. 2226-40
-
-
Frank, A.M.1
-
21
-
-
69349092456
-
ETISEQ-an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics
-
Wong, J. W. H.; Schwahn, A. B.; Downard, K. M. ETISEQ-an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics BMC Bioinform. 2009, 10, 244
-
(2009)
BMC Bioinform.
, vol.10
, pp. 244
-
-
Wong, J.W.H.1
Schwahn, A.B.2
Downard, K.M.3
-
22
-
-
19944432197
-
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
-
Ross, P. L. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents Mol. Cell. Proteomics 2004, 3, 1154-69
-
(2004)
Mol. Cell. Proteomics
, vol.3
, pp. 1154-69
-
-
Ross, P.L.1
-
23
-
-
0036583926
-
Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics
-
Ong, S.-E. Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics Mol. Cell. Proteomics 2002, 1, 376-86
-
(2002)
Mol. Cell. Proteomics
, vol.1
, pp. 376-86
-
-
Ong, S.-E.1
-
24
-
-
0033915395
-
18O-labeled internal standards
-
Mirgorodskaya, O. A.; Kozmin, Y. P.; Titov, M. I.; Körner, R.; Sönksen, C. P.; Roepstorff, P. Quantitation of peptides and proteins by matrix-assisted laser desorption/ionization mass spectrometry using (18)O-labeled internal standards Rapid Commun. Mass Spectrom. 2000, 14, 1226-32 (Pubitemid 30489495)
-
(2000)
Rapid Communications in Mass Spectrometry
, vol.14
, Issue.14
, pp. 1226-1232
-
-
Mirgorodskaya, O.A.1
Kozmin, Y.P.2
Titov, M.I.3
Korner, R.4
Sonksen, C.P.5
Roepstorff, P.6
-
25
-
-
34547112014
-
18O labeling with a correction for labeling efficiency
-
DOI 10.1074/mcp.T600029-MCP200
-
Ramos-Fernaindez, A.; López-Ferrer, D.; Vaizquez, J. Improved method for differential expression proteomics using trypsin-catalyzed 18O labeling with a correction for labeling efficiency Mol. Cell. Proteomics 2007, 6, 1274-86 (Pubitemid 47099235)
-
(2007)
Molecular and Cellular Proteomics
, vol.6
, Issue.7
, pp. 1274-1286
-
-
Ramos-Fernandez, A.1
Lopez-Ferrer, D.2
Vazquez, J.3
-
26
-
-
78651082595
-
MzML - A Community Standard for Mass Spectrometry Data
-
R110.000133
-
Martens, L. mzML-a Community Standard for Mass Spectrometry Data Mol. Cell. Proteomics 2010, R110.000133
-
(2010)
Mol. Cell. Proteomics
-
-
Martens, L.1
-
27
-
-
38649094868
-
The standard protein mix database: A diverse data set to assist in the production of improved peptide and protein identification software tools
-
DOI 10.1021/pr070244j
-
Klimek, J.; Eddes, J. S.; Hohmann, L.; Jackson, J.; Peterson, A.; Letarte, S.; Gafken, P. R.; Katz, J. E.; Mallick, P.; Lee, H.; Schmidt, A.; Ossola, R.; Eng, J. K.; Aebersold, R.; Martin, D. B. The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools J. Proteome Res. 2008, 7, 96-103 (Pubitemid 351171120)
-
(2008)
Journal of Proteome Research
, vol.7
, Issue.1
, pp. 96-103
-
-
Klimek, J.1
Eddes, J.S.2
Hohmann, L.3
Jackson, J.4
Peterson, A.5
Letarte, S.6
Gafken, P.R.7
Katz, J.E.8
Mallick, P.9
Lee, H.10
Schmidt, A.11
Ossola, R.12
Eng, J.K.13
Aebersold, R.14
Martin, D.B.15
-
28
-
-
0034789979
-
Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry
-
DOI 10.1038/nbt1001-946
-
Han, D. K.; Eng, J.; Zhou, H.; Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry Nat. Biotechnol. 2001, 19, 946-51 (Pubitemid 32947573)
-
(2001)
Nature Biotechnology
, vol.19
, Issue.10
, pp. 946-951
-
-
Han, D.K.1
Eng, J.2
Zhou, H.3
Aebersold, R.4
-
29
-
-
0344737959
-
Automated Statistical Analysis of Protein Abundance Ratios from Data Generated by Stable-Isotope Dilution and Tandem Mass Spectrometry
-
DOI 10.1021/ac034633i
-
Li, X.-J.; Zhang, H.; Ranish, J. A.; Aebersold, R. Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry Anal. Chem. 2003, 75, 6648-57 (Pubitemid 37493927)
-
(2003)
Analytical Chemistry
, vol.75
, Issue.23
, pp. 6648-6657
-
-
Li, X.-J.1
Zhang, H.2
Ranish, J.A.3
Aebersold, R.4
-
30
-
-
77949676526
-
A guided tour of the Trans-Proteomic Pipeline
-
Deutsch, E. W.; Mendoza, L.; Shteynberg, D.; Farrah, T.; Lam, H.; Tasman, N.; Sun, Z.; Nilsson, E.; Pratt, B.; Prazen, B.; Eng, J. K.; Martin, D. B.; Nesvizhskii, A. I.; Aebersold, R. A guided tour of the Trans-Proteomic Pipeline Proteomics 2010, 10, 1150-9
-
(2010)
Proteomics
, vol.10
, pp. 1150-9
-
-
Deutsch, E.W.1
Mendoza, L.2
Shteynberg, D.3
Farrah, T.4
Lam, H.5
Tasman, N.6
Sun, Z.7
Nilsson, E.8
Pratt, B.9
Prazen, B.10
Eng, J.K.11
Martin, D.B.12
Nesvizhskii, A.I.13
Aebersold, R.14
-
31
-
-
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, 1367-72
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1367-72
-
-
Cox, J.1
Mann, M.2
-
32
-
-
34547727671
-
High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry
-
DOI 10.1021/ac0700833
-
Hoopmann, M. R.; Finney, G. L.; MacCoss, M. J. High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry Anal. Chem. 2007, 79, 5620-32 (Pubitemid 47229808)
-
(2007)
Analytical Chemistry
, vol.79
, Issue.15
, pp. 5620-5632
-
-
Hoopmann, M.R.1
Finney, G.L.2
MacCoss, M.J.3
|