PXD046928

PXD046928 is an original dataset announced via ProteomeXchange.

Title	Linking Intestinal Microorganisms to their Diet-derived Growth Substrates Using Protein Stable Isotope Fingerprinting (Protein-SIF)
Description	The aim of this study was to directly link intestinal microorganisms to their diet-derived in vivo growth substrates using protein stable isotope fingerprinting (“Protein-SIF”)(Kleiner et al. 2018, PNAS 115(24)). We conducted studies in gnotobiotic mice (C57BL/6J) colonized with a community of 13 human-derived bacterial strains (Desai et al. 2016, Cell 167(5)). There were two groups of mice: group 1 consisted of 5 mice, and group 2 of 6 mice. All mice were fed defined diets modeled on the AIN-93G (EnvigoTeklad) varying in one ingredient source, and a “standard chow” (LabDiet 5010) as a baseline diet before and after the defined diets. Group 1 mice were fed diets differing in protein source (casein, egg whites, soy protein). Group 2 mice were fed diets differing in fiber source (cellulose, inulin, corn fiber), and fat source (corn oil, soybean oil, sunflower oil). Stable carbon isotope ratios for each dietary component were measured using IRMS (table with values is included in submission). Each diet was introduced for 7 days, and fecal samples were collected on the 7th day. We processed samples from the group 1 mice and the group 2 mice as two separate batches. We analyzed the samples by LC-MS/MS. Each sample was run in four consecutive technical replicates to increase the available number of MS1 spectra for SIF calculations. Data were analyzed with Proteome Discoverer followed by the calis-p software for Protein-SIF (https://sourceforge.net/projects/calis-p/). Additionally, this dataset includes diet samples and purified dietary components that were extracted using the same approach as the fecal samples, as well as LC-MS/MS runs of human hair derived peptides used for SIF calibration.
HostingRepository	PRIDE
AnnounceDate	2024-12-16
AnnouncementXML	Submission_2024-12-16_15:04:52.158.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	J. Alfredo Blakeley Ruiz
SpeciesList	scientific name: Agathobacter rectalis DSM 17629; NCBI TaxID: 657318; scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Akkermansia muciniphila ATCC BAA-835; NCBI TaxID: 349741; scientific name: Bacteroides uniformis ATCC 8492; NCBI TaxID: 411479; scientific name: Roseburia intestinalis L1-82; NCBI TaxID: 536231; scientific name: Marvinbryantia formatexigens DSM 14469; NCBI TaxID: 478749; scientific name: [Clostridium] symbiosum WAL-14163; NCBI TaxID: 742740; scientific name: Faecalibacterium prausnitzii M21/2; NCBI TaxID: 411485; scientific name: Bacteroides ovatus ATCC 8483; NCBI TaxID: 411476; scientific name: Barnesiella intestinihominis YIT 11860; NCBI TaxID: 742726; scientific name: Helianthus annuus (Common sunflower); NCBI TaxID: 4232; scientific name: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482); NCBI TaxID: 226186; scientific name: Glycine max; NCBI TaxID: 3847; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Bacteroides caccae ATCC 43185; NCBI TaxID: 411901; scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Collinsella aerofaciens ATCC 25986; NCBI TaxID: 411903; scientific name: Beta vulgaris (Sugar beet); NCBI TaxID: 161934; scientific name: Zea mays subsp. mays (maize); NCBI TaxID: 381124; scientific name: Escherichia coli HS; NCBI TaxID: 331112;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-13 22:20:00	ID requested
⏵ 1	2024-12-16 15:04:52	announced

Dataset with its publication pending

submitter keyword: 1D-LC

mass spectrometry

MS/MS

metaproteomics

metaproteome

microbiota

microbiome

gut

intestinal

fecal

mouse

diet

Protein-SIF.

Manuel Kleiner
contact affiliation	North Carolina State University
contact email	manuel_kleiner@ncsu.edu
lab head
J. Alfredo Blakeley Ruiz
contact affiliation	North Carolina State University, Raliegh, NC
contact email	jablakel@ncsu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD046928
     1. Label: PRIDE project
     2. Name: Linking Intestinal Microorganisms to their Diet-derived Growth Substrates Using Protein Stable Isotope Fingerprinting (Protein-SIF)