Mock microbial community with spike-ins of 13C-labeled Escherichia coli cells for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)

ABSTRACT: This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms in microbial communities after labeling them with stable isotope-labeled substrates. For this dataset Escherichia coli cultures were labeled with different percentages (1, 5 and 10%) of fully labeled 13C glucose (13C1-6) and spiked-in into a mock microbial community consisting of 32 species of bacteria, archaea, eukaryote and bacteriophages (UNEVEN Community described in Kleiner et al. 2017 Nat Communications 8(1):1558). The community also contained unlabeled E. coli cells and labeled/unlabeled E. coli cells in the spike-in sample were at a 1:1 ratio. Cultures of E. coli were grown in M9 minimal medium in which a percentage of the glucose was replaced with 13C1-6 glucose for >10 generations to achieve close to complete labeling of cells. The following percentages of 13C1-6 glucose were added 1, 5 and 10%. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Escherichia Coli

SUBMITTER: Manuel Kleiner  

LAB HEAD: Manuel Kleiner

PROVIDER: PXD024174 | Pride | 2022-12-30

REPOSITORIES: Pride