Simple dual-spotting procedure enhances nLC-MALDI MS/MS analysis of digests with less specific enzymes

Journal of Proteome Research

Volumn 10, Issue 6, 2011, Pages 2889-2894

  Baeumlisberger, Dominic ^a   Rohmer, Marion ^a   Arrey, Tabiwang N ^a   Mueller, Benjamin F ^a   Beckhaus, Tobias ^a   Bahr, Ute ^a   Barka, Guenes ^b   Karas, Michael ^a  

^a GOETHE UNIVERSITY   (Germany)

^b SunChrom Wissenschaftliche Geräte GmbH   (Germany)

Author keywords

elastase; MALDI Orbitrap; nLC; spotting

Indexed keywords

ELASTASE;

ARTICLE; COMPUTER PROGRAM; CORYNEBACTERIUM GLUTAMICUM; CYTOSOL; DATA BASE; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; TANDEM MASS SPECTROMETRY;

BACTERIAL PROTEINS; CALIBRATION; CORYNEBACTERIUM GLUTAMICUM; PEPTIDE FRAGMENTS; PEPTIDE HYDROLASES; REFERENCE STANDARDS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TANDEM MASS SPECTROMETRY;

EID: 79958227897     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr2001644     Document Type: Article

References (23)

1. Gusev, A. I. Interfacing matrix-assisted laser desorption/ionization mass spectrometry with column and planar separations Fresenius J. Anal. Chem. 2000, 366 (6-7) 691-700
2. Nägele, E.; Vollmer, M. Coupling of nanoflow liquid chromatography to matrix-assisted laser desorption/ionization mass spectrometry: real-time liquid chromatography run mapping on a MALDI plate Rapid Commun. Mass Spectrom. 2004, 18 (24) 3008-14 (Pubitemid 39664900)
3. Mirgorodskaya, E.; Braeuer, C.; Fucini, P.; Lehrach, H.; Gobom, J. Nanoflow liquid chromatography coupled to matrix-assisted laser desorption/ionization mass spectrometry: sample preparation, data analysis, and application to the analysis of complex peptide mixtures Proteomics 2005, 5 (2) 399-408 (Pubitemid 40262056)
4. Hattan, S. J.; Marchese, J.; Khainovski, N.; Martin, S.; Juhasz, P. Comparative study of [Three] LC-MALDI workflows for the analysis of complex proteomic samples J. Proteome Res. 2005, 4 (6) 1931-41 (Pubitemid 41814258)
5. Mueller, D. R.; Voshol, H.; Waldt, A.; Wiedmann, B.; Van Oostrum, J. LC-MALDI MS and MS/MS - an efficient tool in proteome analysis Subcell. Biochem. 2007, 43, 355-80
6. Brock, A.; Horn, D. M.; Peters, E. C.; Shaw, C. M.; Ericson, C.; Phung, Q. T.; Salomon, A. R. An automated matrix-assisted laser desorption/ionization quadrupole Fourier transform ion cyclotron resonance mass spectrometer for "bottom-up" proteomics Anal. Chem. 2003, 75 (14) 3419-28 (Pubitemid 36871230)
7. Zhu, K.; Miller, F. R.; Barder, T. J.; Lubman, D. M. Identification of low molecular weight proteins isolated by 2-D liquid separations J. Mass Spectrom. 2004, 39 (7) 770-80 (Pubitemid 39117822)
8. Pan, S.; Rush, J.; Peskind, E. R.; Galasko, D.; Chung, K.; Quinn, J.; Jankovic, J.; Leverenz, J. B.; Zabetian, C.; Pan, C.; Wang, Y.; Oh, J. H.; Gao, J.; Zhang, J.; Montine, T.; Zhang, J. Application of targeted quantitative proteomics analysis in human cerebrospinal fluid using a liquid chromatography matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (LC MALDI TOF/TOF) platform J. Proteome Res. 2008, 7 (2) 720-30 (Pubitemid 351294034)
9. Karas, M.; Hillenkamp, F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 Da Anal. Chem. 1988, 60 (20) 2299-301
10. Hu, Q.; Noll, R. J.; Li, H.; Makarov, A.; Hardman, M.; Graham Cooks, R. The Orbitrap: a new mass spectrometer J. Mass Spectrom. 2005, 40 (4) 430-43 (Pubitemid 40637866)
11. Comisarow, M. B.; Marshall, A. G. Fourier Transform in cyclotron resonance spectroscopy Chem. Phys. Lett. 1974, 25 (2) 282-3
12. Stoop, M. P.; Lamers, R. J.; Burgers, P. C.; Sillevis Smitt, P. A.; Hintzen, R. Q.; Luider, T. M. The rate of false positive sequence matches of peptides profiled by MALDI MS and identified by MS/MS J. Proteome Res. 2008, 7 (11) 4841-7
13. Rietschel, B.; Baeumlisberger, D.; Arrey, T. N.; Bornemann, S.; Rohmer, M.; Schuerken, M.; Karas, M.; Meyer, B. The benefit of combining nLC-MALDI-Orbitrap MS data with nLC-MALDI-TOF/TOF data for proteomic analyses employing elastase J. Proteome Res. 2009, 8 (11) 5317-24
14. Haas, W.; Faherty, B. K.; Gerber, S. A.; Elias, J. E.; Beausoleil, S. A.; Bakalarski, C. E.; Li, X.; Villén, J.; Gygi, S. P. Optimization and use of peptide mass measurement accuracy in shotgun proteomics Mol. Cell. Proteomics 2006, 5 (7) 1326-37 (Pubitemid 44103402)
15. Liu, T.; Belov, M. E.; Jaitly, N.; Qian, W. J.; Smith, R. D. Accurate mass measurements in proteomics Chem. Rev. 2007, 107 (8) 3621-53 (Pubitemid 47322746)
16. Zubarev, R.; Mann, M. On the proper use of mass accuracy in proteomics Mol. Cell. Proteomics 2007, 6 (3) 377-81 (Pubitemid 46554535)
17. Zhang, J.; Ma, J.; Dou, L.; Wu, S.; Qian, X.; Xie, H.; Zhu, Y.; He, F. Mass measurement errors of Fourier-transform mass spectrometry (FTMS): distribution, recalibration, and application J. Proteome Res. 2009, 8 (2) 849-59
18. Clauser, K. R.; Baker, P.; Burlingame, A. L. Role of accurate mass measurement (± 10 ppm) in protein identification strategies employing MS or MS/MS and database searching Anal. Chem. 1999, 71 (14) 2871-82 (Pubitemid 29340480)
19. Wu, C. C.; MacCoss, M. J.; Howell, K. E.; Yates, J. R. A method for the comprehensive proteomic analysis of membrane proteins Nat. Biotechnol. 2003, 21 (5) 532-8 (Pubitemid 36532018)
20. Rietschel, B.; Arrey, T. N.; Meyer, B.; Bornemann, S.; Schuerken, M.; Karas, M.; Poetsch, A. Elastase digests: new ammunition for shotgun membrane proteomics Mol. Cell. Proteomics 2009, 8 (5) 1029-43
21. Schluesener, D.; Fischer, F.; Kruip, J.; Rögner, M.; Poetsch, A. Mapping the membrane proteome of Corynebacterium glutamicum Proteomics 2005, 5 (5) 1317-30
22. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20 (18) 3551-67 (Pubitemid 30007252)
23. Kalinowski, J.; Bathe, B.; Bartels, D.; Bischoff, N.; Bott, M.; Burkovski, A.; Dusch, N.; Eggeling, L.; Eikmanns, B. J.; Gaigalat, L.; Goesmann, A.; Hartmann, M.; Huthmacher, K.; Krämer, R.; Linke, B.; McHardy, A. C.; Meyer, F.; Möckel, B.; Pfefferle, W.; Pühler, A.; Rey, D. A.; Rückert, C.; Rupp, O.; Sahm, H.; Wendisch, V. F.; Wiegräbe, I.; Tauch, A. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins J. Biotechnol. 2003, 104 (1-3) 5-25 (Pubitemid 37011345)