Validating pyAscore, A Python Package for the Localization of Protein Modifications

The submitted dataset contains results of validation experiments for pyAscore, an efficient and versatile implementation of the Ascore algorithm in Python for scoring the localization of user defined PTMs in data dependent mass spectrometry. In order to test the versatility of the package, three samples from three pride accessions were re-analyzed: label-free phosphoprotome samples were downloaded from PXD007740, TMT-labeled phosphoproteome samples were downloaded from PXD007145, and label free acetylome samples were downloaded from MSV000079068. We also wanted to evaluate the performance of pyAscore's PTM localizations on data where the modification site of peptides was known. Thus, we downloaded and re-analyzed synthetic phosphopeptide samples which were analyzed with 3 different fragmentation approaches: HCD and ETD synthetic phosphopeptide data were downloaded from PXD000138 and CID data were downloaded from PXD000759.