Abacus: A tool for extracting and processing spectral count data for label-free quantitative proteomic analysis

摘要

The use of label-free MS based quantification methods have grown in popularity. Spectral counting is one of the most popular methods currently used. In spectral counting, a protein's abundance is inferred based upon the number of tandem mass spectra associated with it following count normalization [1,2]. Several tools have been developed that use spectral counting to identify differentially expressed proteins. All of these programs rely on a matrix of spectral counts as their primary input. In this work we present Abacus, an open-source tool for extracting peptide and spectral counts from the data generated by the TPP. We present the algorithm and a sample data set processed using our tool.