ComPIL 2.0: An Updated Comprehensive Metaproteomics Database

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.