PXD054415-1

PXD054415 is an original dataset announced via ProteomeXchange.

Title	Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome
Description	Metaproteomics used bottom-up mass spectrometry to detect and quantify the proteins present in microbiome samples. Historically, the methodology of choice in these analyses has been Data-Dependent Acquisition mass spectrometry (DDA-MS). In this manuscript we see sought to evaluate the reproducibility and accuracy of data-independent acquisition mass spectrometry (DIA-MS) compared to DDA-MS on samples of known composition.
HostingRepository	PRIDE
AnnounceDate	2024-12-19
AnnouncementXML	Submission_2024-12-19_15:37:32.806.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andrew Rajczewski
SpeciesList	scientific name: Thermus thermophilus; NCBI TaxID: 274; scientific name: unclassified Bacillus subtilis group; NCBI TaxID: 2750820; scientific name: Nitrosomonas ureae; NCBI TaxID: 44577; scientific name: Desulfovibrio vulgaris str. Hildenborough; NCBI TaxID: 882; scientific name: Escherichia phage M13; NCBI TaxID: 2785248; scientific name: Cupriavidus metallidurans; NCBI TaxID: 119219; scientific name: Enterobacteria phage ES18; NCBI TaxID: 101570; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2; scientific name: Stenotrophomonas maltophilia; NCBI TaxID: 40324; scientific name: Chromobacterium violaceum; NCBI TaxID: 536; scientific name: Enterobacteria phage f2; NCBI TaxID: 12016; scientific name: Paracoccus denitrificans; NCBI TaxID: 266; scientific name: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720); NCBI TaxID: 99287; scientific name: Salmonella phage P22; NCBI TaxID: 2908168; scientific name: Anthracocystis tumefaciens; NCBI TaxID: 249467; scientific name: Staphylococcus aureus; NCBI TaxID: 1280; scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Nitrosospira multiformis; NCBI TaxID: 1231; scientific name: Roseobacter; NCBI TaxID: 2433; scientific name: unclassified Pseudomonas fluorescens group; NCBI TaxID: 2775505; scientific name: Paraburkholderia xenovorans; NCBI TaxID: 36873; scientific name: Pseudomonas cf. pseudoalcaligenes; NCBI TaxID: 136404; scientific name: Alteromonas macleodii; NCBI TaxID: 28108; scientific name: Archaea; NCBI TaxID: NCBITaxon:2157; scientific name: Rhizobium leguminosarum; NCBI TaxID: 384; scientific name: Chlamydomonas reinhardtii; NCBI TaxID: 3055; scientific name: Nitrososphaera viennensis; NCBI TaxID: 1034015; scientific name: Pseudomonas denitrificans (nom. rej.); NCBI TaxID: 43306;
ModificationList	deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse; Q Exactive; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-30 17:57:46	ID requested
⏵ 1	2024-12-19 15:37:33	announced

10.1101/2024.09.18.613707;

Rajczewski AT, Blakeley-Ruiz JA, Meyer A, Vintila S, McIlvin MR, Van Den Bossche T, Searle BC, Griffin TJ, Saito MA, Kleiner M, Jagtap PD, Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome. bioRxiv, ():(2025) [pubmed]

submitter keyword: data independent acquisition,microbiome, metaproteomics

Timothy J Griffin
contact affiliation	Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota
contact email	tgriffin@umn.edu
lab head
Andrew Rajczewski
contact affiliation	University of Minnesota
contact email	rajcz001@umn.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/12/PXD054415

PRIDE project URI

• PRIDE
  1. PXD054415
     1. Label: PRIDE project
     2. Name: Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome