Improving proteomics mass accuracy by dynamic offline lock mass

Analytical Chemistry

Volumn 83, Issue 24, 2011, Pages 9344-9351

  Zhang, Ying ^a   Wen, Zhihui ^a   Washburn, Michael P ^a,b   Florens, Laurence ^a  

^a STOWERS INSTITUTE FOR MEDICAL RESEARCH   (United States)

^b UNIVERSITY OF KANSAS SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSTRACTION METHODS; AMBIENT CONDITIONS; ANALYTE IONS; CALIBRANTS; DATA SETS; DYNAMIC FEATURES; DYNAMIC RANGE; ELECTROSPRAYS; MASS ACCURACY; MASS CALIBRATIONS; OFFLINE; PRECURSOR IONS; PROTEIN SAMPLES; PROTEOMICS; PROTONATED; RECALIBRATIONS; STATISTICAL TREATMENT; TANDEM MASS SPECTROSCOPY;

MASS SPECTROMETRY; MOLECULAR BIOLOGY;

IONS;

ION; PROTEIN; SILOXANE;

ARTICLE; CHEMISTRY; MOLECULAR WEIGHT; PROTEOMICS; TANDEM MASS SPECTROMETRY;

IONS; MOLECULAR WEIGHT; PROTEINS; PROTEOMICS; SILOXANES; TANDEM MASS SPECTROMETRY;

EID: 83655164803     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac201867h     Document Type: Article

References (23)

1. Charles, L. Flow injection of the lock mass standard for accurate mass measurement in electrospray ionization time-of-flight mass spectrometry coupled with liquid chromatography Rapid Commun. Mass Spectrom. 2003, 17 (13) 1383-1388
2. Olsen, J. V.; de Godoy, L. M.; Li, G.; Macek, B.; Mortensen, P.; Pesch, R.; Makarov, A.; Lange, O.; Horning, S.; Mann, M. Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap Mol. Cell. Proteomics 2005, 4 (12) 2010-2021
3. Haas, W.; Faherty, B. K.; Gerber, S. A.; Elias, J. E.; Beausoleil, S. A.; Bakalarski, C. E.; Li, X.; Villen, J.; Gygi, S. P. Optimization and use of peptide mass measurement accuracy in shotgun proteomics Mol. Cell. Proteomics 2006, 5 (7) 1326-1337
4. Petyuk, V. A.; Mayampurath, A. M.; Monroe, M. E.; Polpitiya, A. D.; Purvine, S. O.; Anderson, G. A.; Camp, D. G., 2nd; Smith, R. D. DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets Mol. Cell. Proteomics 2010, 9 (3) 486-496
5. Wenger, C. D.; McAlister, G. C.; Xia, Q.; Coon, J. J. Sub-part-per-million precursor and product mass accuracy for high-throughput proteomics on an electron transfer dissociation-enabled orbitrap mass spectrometer Mol. Cell. Proteomics 2010, 9 (5) 754-763
6. Schlosser, A.; Volkmer-Engert, R. Volatile polydimethylcyclosiloxanes in the ambient laboratory air identified as source of extreme background signals in nanoelectrospray mass spectrometry J. Mass Spectrom. 2003, 38 (5) 523-525
7. Florens, L.; Washburn, M. P. Proteomic analysis by multidimensional protein identification technology Methods Mol. Biol. 2006, 328, 159-175
8. Zhang, Y.; Wen, Z.; Washburn, M. P.; Florens, L. Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins Anal. Chem. 2010, 82 (6) 2272-2281
9. Sato, S.; Tomomori-Sato, C.; Parmely, T. J.; Florens, L.; Zybailov, B.; Swanson, S. K.; Banks, C. A.; Jin, J.; Cai, Y.; Washburn, M. P.; Conaway, J. W.; Conaway, R. C. A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology Mol. Cell 2004, 14 (5) 685-691
10. Galassi, M.; Davies, J.; Theiler, J.; Gough, B.; Jungman, G.; Alken, P.; Booth, M.; Rossi, F. GNU Scientific Library Reference Manual: Network Theory Ltd.: U.K., 2009; p 592.
11. McDonald, W. H.; Tabb, D. L.; Sadygov, R. G.; MacCoss, M. J.; Venable, J.; Graumann, J.; Johnson, J. R.; Cociorva, D.; Yates, J. R., III. MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications Rapid Commun. Mass Spectrom. 2004, 18 (18) 2162-2168
12. Mayampurath, A. M.; Jaitly, N.; Purvine, S. O.; Monroe, M. E.; Auberry, K. J.; Adkins, J. N.; Smith, R. D. DeconMSn: A software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra Bioinformatics 2008, 24 (7) 1021-1023
13. Eng, J.; McCormack, A. L.; Yates, J. R., III. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database J. Am. Mass Spectrom. 1994, 5, 976-989
14. Zubarev, R.; Mann, M. On the proper use of mass accuracy in proteomics Mol. Cell. Proteomics 2007, 6 (3) 377-381
15. Mosley, A. L.; Florens, L.; Wen, Z.; Washburn, M. P. A label free quantitative proteomic analysis of the Saccharomyces cerevisiae nucleus J. Proteomics 2009, 72 (1) 110-120
16. Graumann, J.; Hubner, N. C.; Kim, J. B.; Ko, K.; Moser, M.; Kumar, C.; Cox, J.; Scholer, H.; Mann, M. Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins Mol. Cell. Proteomics 2008, 7 (4) 672-683
17. Mo, L.; Dutta, D.; Wan, Y.; Chen, T. MSNovo: A dynamic programming algorithm for de novo peptide sequencing via tandem mass spectrometry Anal. Chem. 2007, 79 (13) 4870-4878
18. Petyuk, V. A.; Jaitly, N.; Moore, R. J.; Ding, J.; Metz, T. O.; Tang, K.; Monroe, M. E.; Tolmachev, A. V.; Adkins, J. N.; Belov, M. E.; Dabney, A. R.; Qian, W.-J.; Camp, D. G.; Smith, R. D. Elimination of Systematic Mass Measurement Errors in Liquid Chromatography-Mass Spectrometry Based Proteomics Using Regression Models and a Priori Partial Knowledge of the Sample Content Anal. Chem. 2007, 80 (3) 693-706
19. Bereman, M. S.; Williams, T. I.; Muddiman, D. C. Development of a nanoLC LTQ Orbitrap Mass Spectrometric Method for Profiling Glycans Derived from Plasma from Healthy, Benign Tumor Control, and Epithelial Ovarian Cancer Patients Anal. Chem. 2008, 81 (3) 1130-1136
20. Tsur, D.; Tanner, S.; Zandi, E.; Bafna, V.; Pevzner, P. A. Identification of post-translational modifications by blind search of mass spectra Nat. Biotechnol. 2005, 23 (12) 1562-1567
21. Cooper, B. The Problem with Peptide Presumption and Low Mascot Scoring J. Proteome Res. 2011, 10 (3) 1432-1435
22. Hsieh, E. J.; Hoopmann, M. R.; MacLean, B.; MacCoss, M. J. Comparison of Database Search Strategies for High Precursor Mass Accuracy MS/MS Data J. Proteome Res. 2009, 9 (2) 1138-1143
23. Martens, L.; Chambers, M.; Sturm, M.; Kessner, D.; Levander, F.; Shofstahl, J.; Tang, W. H.; Rompp, A.; Neumann, S.; Pizarro, A. D.; Montecchi-Palazzi, L.; Tasman, N.; Coleman, M.; Reisinger, F.; Souda, P.; Hermjakob, H.; Binz, P. A.; Deutsch, E. W. mzML-A community standard for mass spectrometry data Mol. Cell. Proteomics 2011, 10 (1) R110 000133