MetaNovo: a probabilistic approach to peptide discovery in complex metaproteomic datasets

Abstract

Town, Cape Town, South Africa.UniProt we achieved a comparable MS/MS identification rate during target-decoy search to using the UniProt human Reference proteome, with 22583 ( 85.99 %) of the total set of identified peptides shared in common. Taxonomic analysis of 612 peptides not found in the canonical set of human proteins yielded 158 peptides unique to the Chordata phylum as potential human variant identifications. Of these, 40 had previously been predicted and 9 identified using whole genome sequencing in a proteogenomic study of the same cell-line. By estimating taxonomic and peptide level information on microbiome samples directly from tandem mass spectrometry data, MetaNovo enables simultaneous identification of human, bacterial, helminth, fungal, viral and other eukaryotic proteins in a sample, thus allowing correlations between changes in microbial protein abundance and change in the host proteome to be drawn based on a single analysis. Data are available via ProteomeXchange with identifier PXD014214 . The MetaNovo software is available from GitHub and can be run as a standalone Singularity or Docker 2 container available from the Docker Hub .3

Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression

“…Proteomic data were used to infer vaginal microbiome composition and host secretome as described previously [45]. Briefly, proteins were identified using two different databases: (i) UniProt database restricted to human and microbial entries (73,910,451, release August 2017) and filtered using the MetaNovo pipeline [48] and (ii) human proteins combined with a vaginal metagenome-based database obtained from the study of Afiuni-Zadeh et al [49]. Taxonomy was assigned using UniProt, and relative abundance of each taxon was determined by aggregating the intensity-based absolute quantification (iBAQ) values of all proteins identified for each taxon.…”

A pilot study to show that asymptomatic sexually transmitted infections alter the foreskin epithelial proteome

“…Maxquant software package version 1.5.0.3 with integrated Andromeda search engine was used to analyze the raw MS spectra (Cox and Mann, 2008) search against a UniProt human and microbial protein database (ca. 65 million entries; July 2017 release) filtered using the MetaNovo pipeline 1 and concatenated with the human reference proteome to create a database of 146,885 entries, as previously described (Potgieter et al, 2019; 1 https://anaconda.org/bioconda/metanovo Frontiers in Microbiology 04 frontiersin.org LC-MS-based proteomics of foreskin samples and data analysis methods used to assess the impact of aSTI on the foreskin proteome. (A) Equal mass of inner and outer foreskin samples were dissected, and proteins were solubilized and digested with trypsin enzyme to create peptides that were analyzed by LC-MS. In-gel digestion method, FASP, and in-solution digestion methods were performed to determine the appropriate method for foreskin peptide generation.…”

Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification

“…52 All of these techniques have advantages and drawbacks, and the interested reader is referred to the large amount of literature in this area. 53,54 Recently, Potgieter et al 55 published a method called MetaNovo which uses de novo sequence tags to identify peptides from a very large database. MetaNovo uses DeN-ovoGui 56 to run DirecTag 34 to create de novo sequence tags.…”

“…Recently, Potgieter et al 55 published a method called MetaNovo which uses de novo sequence tags to identify peptides from a very large database. MetaNovo uses DeNovoGui 56 to run DirecTag 34 to create de novo sequence tags.…”