Automated quality control system for LC-SRM setups

Journal of Proteomics

Volumn 95, Issue , 2013, Pages 77-83

  Teleman, Johan ^a   Waldemarson, Sofia ^a   Malmström, Johan ^a   Levander, Fredrik ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

Mass spectrometry; Quality control; Selected reaction monitoring; Software; Targeted proteomics

Indexed keywords

PEPTIDE FRAGMENT; PROTEIN;

ARTICLE; COMPUTER PROGRAM; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; QUALITY CONTROL; SELECTED REACTION MONITORING; WORKFLOW;

MASS SPECTROMETRY; QUALITY CONTROL; SELECTED REACTION MONITORING; SOFTWARE; TARGETED PROTEOMICS;

AUTOMATION, LABORATORY; PROTEOMICS; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84888291700     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.03.029     Document Type: Article

References (19)

1. Picotti P., Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods 2012, 9:555-566.
2. Stahl-Zeng J., Lange V., Ossola R., Eckhardt K., Krek W., Aebersold R, et al. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics 2007, 6:1809-1817.
3. Schmidt A., Karas M., Dülcks T. Effect of different solution flow rates on analyte ion signals in nano-ESI MS, or: when does ESI turn into nano-ESI?. J Am Soc Mass Spectrom 2003, 14:492-500.
4. Tang X., Bruce J.E., Hill H.H. Characterizing electrospray ionization using atmospheric pressure ion mobility spectrometry. Anal Chem 2006, 78:7751-7760.
5. El-Faramawy A., Siu K.W.M., Thomson B.A. Efficiency of nano-electrospray ionization. J Am Soc Mass Spectrom 2005, 16:1702-1707.
6. Eyers C.E., Simpson D.M., Wong S.C.C., Beynon R.J., Gaskell S.J. QCAL - a novel standard for assessing instrument conditions for proteome analysis. J Am Soc Mass Spectrom 2008, 19:1275-1280.
7. Burkhart J.M., Premsler T., Sickmann A. Quality control of nano-LC-MS systems using stable isotope-coded peptides. Proteomics 2011, 11:1049-1057.
8. Abbatiello Susan E., Mani D.R., Schilling B., MacLean B., Zimmerman L.J., Feng X., et al. Design, implementation and multi-site evaluation of a system suitability protocol for the quantitative assessment of instrument performance in LC-MRM-MS 2013, (submitted for publication).
9. Rudnick P.A., Clauser K.R., Kilpatrick L.E., Tchekhovskoi D.V., Neta P., Blonder N., et al. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol Cell Proteomics 2010, 9:225-241.
10. Klimek J., Mason C., Vincent-Maloney N. Troubleshooting LTQ and LTQ-Orbitrap LC-MS/MS systems with MassQC. J Biomol Tech 2010, 21:S37.
11. Ma Z.-Q., Polzin K.O., Dasari S., Chambers M.C., Schilling B., Gibson B.W., et al. QuaMeter: multivendor performance metrics for LC-MS/MS proteomics instrumentation. Anal Chem 2012, 84:5845-5850.
12. Sweredoski M.J., Smith G.T., Kalli A., Graham R.L.J., Hess S. LogViewer: a software tool to visualize quality control parameters to optimize proteomics experiments using Orbitrap and LTQ-FT mass spectrometers. J Biomol Tech 2011, 22:122-126.
13. RawMeat online at. http://vastsci.com/rawmeat/.
14. Pichler P., Mazanek M., Dusberger F., Weilnböck L., Huber C.G., Stingl C., 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.
15. Teleman J., Karlsson C., Waldemarson S., Hansson K., James P., Malmström J., et al. Automated selected reaction monitoring software for accurate label-free protein quantification. J Proteome Res 2012, 11:3766-3773.
16. Martens L., Chambers M., Sturm M., Kessner D., Levander F., Shofstahl J., et al. mzML - a community standard for mass spectrometry data. Mol Cell Proteomics 2011, 10. :R110.000133.
17. Kessner D., Chambers M., Burke R., Agus D., Mallick P. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 2008, 24:2534-2536.
18. America A.H., Cordewener J.H., van Geffen M.H., Lommen A., Vissers J.P., Bino R.J., et al. Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC-MS. Proteomics 2006, 6:641-653.
19. Mueller L.N., Rinner O., Schmidt A., Letarte S., Bodenmiller B., Brusniak M.Y., et al. SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 2007, 7:3470-3480.