Modern mass spectrometry-based proteomics enables the identification and quantification of thousands of proteins. Therefore, quantitative mass spectrometry represents an indispensable technology for biological and clinical research. Statistical analyses are required for the unbiased answering of scientific questions and to uncover all important information in the proteomic data. In this training we will cover the full analysis workflow from label-free, data dependent acquisition (DDA) raw data to statistical results. We’ll use two popular quantitative proteomics software: MaxQuant and MSstats.

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• Learn how to use MaxQuant and MSstats for the analysis of label-free shotgun (DDA) data