Institute of Information Science, Academia Sinica

Mass spectrometry-based analysis of proteins and proteomes has become increasingly more quantitative. Current proteomics workflows are also very diverse in terms of experimental approaches, methods of extracting quantitative information, and how the quantitative information is utilized in the experiment. This presentation will start with a general overview of quantitative proteomics and critical examination of different quantitative mass spectrometry methods. Our focus will be on accurate interpretation of quantitative data and on understanding advantages and limitations of different approaches. We will illustrate the discussion using our own recent studies, including the reconstruction of protein interaction networks using affinity purification – mass spectrometry (AP-MS) data, integrative analysis of data from different mass spectrometry platforms, benchmarking of label-free quantification methods, and comparative analysis of absolute protein and mRNA abundance data.