ComPIL 2.0: An Updated Comprehensive Metaproteomics Database

Sung Kyu Robin Park, Titus Jung, Peter S. Thuy-Boun, Ana Y. Wang, John R. Yates, Dennis W. Wolan

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


We designed a metaproteomic analysis method (ComPIL) to accommodate the ever-increasing number of sequences against which experimental shotgun proteomics spectra could be accurately and rapidly queried. Our objective was to create these large databases for the analysis of complex metasamples with unknown composition, including those derived from human, animal, and environmental microbiomes. The amount of high-throughput sequencing data has substantially increased since our original database was assembled in 2014. Here, we present a rebuild of the ComPIL libraries comprised of updated publicly disseminated sequence data as well as a modified version of the search engine ProLuCID-ComPIL optimized for querying experimental spectra. ComPIL 2.0 consists of 113 million protein records and roughly 4.8 billion unique tryptic peptide sequences and is 2.3 times the size of our original version. We searched a data set collected on a healthy human gut microbiome proteomic sample and compared the results to demonstrate that ComPIL 2.0 showed a substantial increase in the number of unique identified peptides and proteins compared to the first ComPIL version. The high confidence of protein identification and accuracy demonstrated by the use of ComPIL 2.0 may encourage the method's application for large-scale proteomic annotation of complex protein systems.

Original languageEnglish
Pages (from-to)616-622
Number of pages7
JournalJournal of Proteome Research
Issue number2
StatePublished - 1 Feb 2019
Externally publishedYes


  • ComPIL
  • ProLuCID
  • metaproteomics
  • microbiome
  • proteomics search engine


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