ComPIL

ComPIL (Comprehensive Protein Identification Library) is a metaproteomic analysis method to address the challenges of querying experimental shotgun proteomics spectra against an ever-expanding number of sequences. The primary goal behind the development of ComPIL was to construct large databases capable of analyzing complex metasamples of unknown composition. These samples could originate from diverse sources, including human, animal, and environmental microbiomes, reflecting the method's versatility and broad applicability in metaproteomic research.

With the substantial growth in high-throughput sequencing data since the initial assembly of the original database in 2014, there was a pressing need to update and enhance the ComPIL libraries. The latest iteration, ComPIL 2.0, incorporates updated publicly available sequence data and features a modified version of the search engine ProLuCID-ComPIL, which is optimized for querying experimental spectra. This update has significantly expanded the library's capacity, with ComPIL 2.0 containing 113 million protein records and approximately 4.8 billion unique tryptic peptide sequences—making it 2.3 times larger than its predecessor.