Reanalysis of PXD024291

This repository contains a dataset analyzed in "De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution".

Specifically, this repository contains the reanalysis of the protein-SIP data obtained from PXD024291 ("Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities using protein-based stable isotope probing proteomics (Protein-SIP)") that was published in Kleiner M, Kouris A, Violette M, D'Angelo G, Liu Y, Korenek A, Tolić N, Sachsenberg T, McCalder J, Lipton MS, Strous M. Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. Microbiome. 2023 11(1):24 based on data from Starke R, Oliphant K, Jehmlich N, Schäpe SS, Sachsenberg T, Kohlbacher O, et al. Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. J Proteomics. 2020;222:103791.

mztab files originate from Casanovo

tsv files originate from PepNet

xlsx files originate from merging Unipept and MetaProSIP output and BLASTp of peptides not referenced in the reference database nor UniProt.