An exclusion list based label-free proteome quantification approach using an LTQ Orbitrap

Rapid Communications in Mass Spectrometry : RCM
Jan MuntelDörte Becher

Abstract

Label-based mass spectrometry is a powerful tool for large-scale protein identification and quantification. However, it requires the chemical or metabolic incorporation of the labeled compound(s) which can be difficult to attain, e.g. for non-cultivable organisms or scarce sample, such as biopsies. Therefore, we set out to develop and validate an efficient label-free liquid chromatography/tandem mass spectrometry (LC/MS/MS) workflow based on optimized instrument settings and incremental exclusion lists. To increase the number of quantified peptides an incremental exclusion list was incorporated along with optimized instrument settings for the used LTQ Orbitrap. As a proof of concept, label-free quantification data from this optimized approach were compared to the results of control measurements without exclusion lists and of an in vivo metabolic labeling GeLC/MS/MS experiment. The data were drawn from Staphylococcus aureus whole cell lysates of non-stressed and nitric oxide (NO)-stressed cells. Compared to MS analysis without exclusion lists the new approach resulted in an increased number of identified peptides, enabling label-free quantification of more than 990 S. aureus proteins. With respect to the number of quantified pro...Continue Reading

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Citations

Dec 13, 2012·Molecular & Cellular Proteomics : MCP·Francesco BonardiJan Jacob Schuringa
Jan 25, 2014·International Journal of Medical Microbiology : IJMM·Katrin BäsellDörte Becher
Apr 12, 2014·International Journal of Proteomics·Saša KončarevićHans-Dieter Zucht
Dec 15, 2015·Expert Review of Proteomics·Maja Semanjski, Boris Macek
Dec 3, 2014·Rapid Communications in Mass Spectrometry : RCM·Jeonghun YeomCheolju Lee
Jan 1, 2014·Proteomics·Andreas OttoFrank Schmidt
Mar 19, 2013·Journal of Proteomics·Kelly HodgeAngus I Lamond
May 16, 2014·Nucleus·Mercè PamblancoSusana Rodríguez-Navarro
Jun 28, 2016·Scientific Reports·Daniela ZühlkeMichael Hecker
Apr 17, 2013·Journal of Proteome Research·David C DallasCarlito B Lebrilla
Oct 25, 2016·Nature Microbiology·Sten KönigStephanie Markert

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