OpenASChem: A Data Analysis Software Suite for High-Throughput Affinity Selection Mass Spectrometry

Summary: Affinity selection mass spectrometry (AS-MS) enables ligand discovery from pooled compound libraries, but compound signal assignment and cross-run review remain labor-intensive as screens expand across multiple targets. Here, we present OpenASChem, an open-source platform with a graphical interface for compoundcentric analysis of high-throughput pull-down ASMS screens. OpenASChem integrates standardguided peak matching, cross-run quantification and enrichment analysis with interactive chromatographic review. We evaluated OpenASChem using mixed-standard and AS-MS screening datasets acquired in our laboratory. In the mixed-standard benchmark, OpenASChem recovered 248 expectedpositive compounds compared with 204 using an XCMS-based workflow, a 21.6% increase, with no calls from the two pools expected to remain below the enrichment threshold. In a four-pool ASMS screen against eight proteins, it reported 13 candidate associations, including all five previously reported hits and two additional chromatographically supported candidates, while reducing candidates not supported by manual review by 86.7%. An interactive summary integrates results across pools and targets, helping laboratories assess chromatographic evidence and prioritize compounds for follow-up validation.