DOI: 10.1021/pr050300l. Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics

Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics

10.1021/pr050300l

Crossref journal-article

American Chemical Society (ACS)

Journal of Proteome Research (316)

Bibliography

Callister, S. J., Barry, R. C., Adkins, J. N., Johnson, E. T., Qian, W., Webb-Robertson, B.-J. M., Smith, R. D., & Lipton, M. S. (2006). Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics. Journal of Proteome Research, 5(2), 277â286.

Authors 8

Stephen J. Callister (first)
Richard C. Barry (additional)
Joshua N. Adkins (additional)
Ethan T. Johnson (additional)
Wei-jun Qian (additional)
Bobbie-Jo M. Webb-Robertson (additional)
Richard D. Smith (additional)
Mary S. Lipton (additional)

References 31 Referenced 396

10.1073/pnas.172170199 / Proc. Natl. Acad. Sci. U.S.A. by Lipton M. S. (2002)
10.1002/1615-9861(200205)2:5<513::AID-PROT513>3.0.CO;2-W / Proteomics by Smith R. D. (2002)
10.1021/ja991063o / J. Am. Chem. Soc. by Pasa-Tolic L. (1999)
{'key': 'pr050300lb00004/pr050300lb00004_1', 'first-page': '999', 'volume': '17', 'author': 'Gygi S. P.', 'year': '1999', 'journal-title': 'Nat. Biotechnol.'} / Nat. Biotechnol. by Gygi S. P. (1999)
{'key': 'pr050300lb00005/pr050300lb00005_1', 'first-page': '4979', 'volume': '74', 'author': 'Qiu Y. C.', 'year': '2002', 'journal-title': 'Anal. Chem.'} / Anal. Chem. by Qiu Y. C. (2002)
10.1002/rcm.362 / Rapid Commun. Mass Spectrom. by Goodlett D. R. (2001)
10.1093/bioinformatics/btg083 / Bioinformatics by Edwards D. (2003)
10.1002/mas.10048 / Mass Spectrom. Rev. by Lill J. (2003)
Goodlett, D. R.; Yi, E. C.Trac-Trends Anal. Chem.2003,22, 282−+. (10.1016/S0165-9936(03)00505-3)
{'key': 'pr050300lb00010/pr050300lb00010_1', 'first-page': '278', 'volume': '37', 'author': 'Smith R. D.', 'year': '2004', 'journal-title': 'Accounts Chem. Res.'} / Accounts Chem. Res. by Smith R. D. (2004)
{'key': 'pr050300lb00011/pr050300lb00011_1', 'first-page': '1423', 'volume': '15', 'author': 'Tang K. Q.', 'year': '2004', 'journal-title': 'J. Am. Soc. Mass Spectrom.'} / J. Am. Soc. Mass Spectrom. by Tang K. Q. (2004)
10.1002/(SICI)1097-0231(19990730)13:14<1427::AID-RCM662>3.0.CO;2-5 / Rapid Commun. Mass Spectrom. by Voyksner R. D. (1999)
{'key': 'pr050300lb00013/pr050300lb00013_1', 'first-page': '30', 'author': 'Yang Y. H.', 'year': '2002', 'journal-title': 'Nucleic Acids Res.'} / Nucleic Acids Res. by Yang Y. H. (2002)
{'key': 'pr050300lb00014/pr050300lb00014_1', 'first-page': '4', 'author': 'Park T.', 'year': '2003', 'journal-title': 'Bmc Bioinformatics'} / Bmc Bioinformatics by Park T. (2003)
10.1080/01621459.1979.10481038 / J. Am. Stat. Assoc. by Cleveland W. S. (1979)
10.1093/bioinformatics/19.2.185 / Bioinformatics by Bolstad B. M. (2003)
10.1016/S0006-8993(97)00548-9 / Brain Res. by Melega W. P. (1997)
10.1016/j.jasms.2003.09.008 / J. Am. Soc. Mass Spectrom. by Belov M. E. (2004)
{'key': 'pr050300lb00019/pr050300lb00019_1', 'first-page': '139', 'volume': '12', 'author': 'Dudoit S.', 'year': '2002', 'journal-title': 'Stat. Sin.'} / Stat. Sin. by Dudoit S. (2002)
10.2144/02326mt02 / Biotechniques by Colantuoni C. (2002)
10.1038/ng1032 / Nat. Genet. by Quackenbush J. (2002)
{'key': 'pr050300lb00022/pr050300lb00022_1', 'first-page': '125', 'volume': '120', 'author': 'Schadt E. E.', 'year': '2001', 'journal-title': 'J. Cell. Biochem.'} / J. Cell. Biochem. by Schadt E. E. (2001)
10.1093/nar/29.12.2549 / Nucleic Acids Res. by Tseng G. C. (2001)
10.1016/S1046-2023(03)00155-5 / Methods by Smyth G. K. (2003)
{'key': 'pr050300lb00025/pr050300lb00025_1', 'volume-title': 'An Introduction to Statistical Methods and Data Analysis', 'author': 'Ott L. R.', 'year': '2001', 'edition': '5'} / An Introduction to Statistical Methods and Data Analysis by Ott L. R. (2001)
{'key': 'pr050300lb00026/pr050300lb00026_1', 'first-page': '1347', 'volume': '19', 'author': 'Wang X. J.', 'year': '2003', 'journal-title': 'Bioinformatics'} / Bioinformatics by Wang X. J. (2003)
10.1021/ac049043e / Anal. Chem. by Masselon C. (2005)
10.1021/ac0342572 / Anal. Chem. by Mohan D. (2003)
10.1016/S0168-1656(99)00163-7 / J. Biotechnol. by Thellin O. (1999)
{'key': 'pr050300lb00030/pr050300lb00030_1', 'volume-title': 'Symp. Biocomput.', 'author': 'Wang P.', 'year': '2005'} / Symp. Biocomput. by Wang P. (2005)
{'key': 'pr050300lb00031/pr050300lb00031_1', 'first-page': '4826', 'volume': '75', 'author': 'Wang W. X.', 'year': '2003', 'journal-title': 'Anal. Chem.'} / Anal. Chem. by Wang W. X. (2003)

Dates

Type	When
Created	19 years, 6 months ago (Feb. 3, 2006, 12:33 a.m.)
Deposited	3 years, 10 months ago (Oct. 10, 2021, 10:54 a.m.)
Indexed	26 minutes ago (Aug. 31, 2025, 5:31 a.m.)
Issued	19 years, 7 months ago (Jan. 17, 2006)
Published	19 years, 7 months ago (Jan. 17, 2006)
Published Online	19 years, 7 months ago (Jan. 17, 2006)
Published Print	19 years, 6 months ago (Feb. 1, 2006)

Funders 0

None

BibTeX

@article{Callister_2006, title={Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics}, volume={5}, ISSN={1535-3907}, url={http://dx.doi.org/10.1021/pr050300l}, DOI={10.1021/pr050300l}, number={2}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Callister, Stephen J. and Barry, Richard C. and Adkins, Joshua N. and Johnson, Ethan T. and Qian, Wei-jun and Webb-Robertson, Bobbie-Jo M. and Smith, Richard D. and Lipton, Mary S.}, year={2006}, month=jan, pages={277–286} }

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