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updated FragPipe import function; now uses quantitative data from the MSstats.csv file instead of collecting data across all ion.tsv files. This should ensure we use the intended output/filtered quantitative data and make our import function more robust (backtested on all major FragPipe releases from 14.0 to 22.0). Specifically, we import precursor ion intensities from MSstats.csv for all precursor*sample pairs, then search for respective PSM confidence scores and retention times in the psm.tsv files (not available for MBR hits)
bugfix for parsing FASTA files that contain decoy/reverse entries; decoys are now properly recognized and only target proteins are imported into MS-DAP