Abstract
Recently, new software tools have been developed for improved protein quantification using mass spectrometry (MS) data. However, there are still limitations especially in high-sample-throughput quantification methods, and most of these relate to extensive computational calculations. The mass accuracy precursor alignment (MAPA) strategy has been shown to be a robust method for relative protein quantification. Its major advantages are high resolution, sensitivity and sample throughput. Its accuracy is data dependent and thus best suited for precursor mass-to-charge precision of ∼1 p.p.m. This protocol describes how to use a software tool (ProtMAX) that allows for the automated alignment of precursors from up to several hundred MS runs within minutes without computational restrictions. It comprises features for 'ion intensity count' and 'target search' of a distinct set of peptides. This procedure also includes the recommended MS settings for complex quantitative MAPA analysis using ProtMAX (http://www.univie.ac.at/mosys/software.html).
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Acknowledgements
We thank J. Hummel for interesting comments.
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V.E. developed the algorithm of the ProtMAX tool. W.H. contributed to the concept and optimization of the ProtMAX tool of protein analysis and writing of the manuscript. D.L. contributed to the concept of the ProtMAX tool and writing of the manuscript. W.W. conceived the concept of the MAPA strategy for proteomics. S.W. conceived Preferences and feature upgrading with the target approach of the ProtMAX tool and was responsible for project coordination and writing of the manuscript.
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Egelhofer, V., Hoehenwarter, W., Lyon, D. et al. Using ProtMAX to create high-mass-accuracy precursor alignments from label-free quantitative mass spectrometry data generated in shotgun proteomics experiments. Nat Protoc 8, 595–601 (2013). https://doi.org/10.1038/nprot.2013.013
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DOI: https://doi.org/10.1038/nprot.2013.013
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