PXD039581

PXD039581 is an original dataset announced via ProteomeXchange.

Title	ChipFilter: Microfluidic Based Comprehensive Sample Preparation Methodology for Metaproteomics
Description	Here, we show that a ChipFilter microfluidic device coupled to LC-MS/MS can successfully be used for identification of microbial proteins. Using cultures of E. coli, B. subtilis and S. cerevisiae, we have shown that it is possible to directly lyse the cells and digest the proteins in the ChipFilter to allow higher number of proteins and peptides identification than standard protocols, even at low cell density. The peptides produced are overall longer after ChipFilter digestion but show no change in their degree of hydrophobicity. Analysis of a more complex mixture of 17 species from the gut microbiome showed that the ChipFilter preparation was able to identify and estimate the amount of 16 of these species.
HostingRepository	PRIDE
AnnounceDate	2024-05-24
AnnouncementXML	Submission_2024-05-24_02:43:03.926.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yann Verdier
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-20 02:40:14	ID requested
⏵ 1	2024-05-24 02:43:04	announced

10.1021/acs.jproteome.3c00288;

Ravi Kumar RK, Ndiaye MM, Haddad I, Vinh J, Verdier Y, ChipFilter: Microfluidic-Based Comprehensive Sample Preparation Methodology for Microbial Consortia. J Proteome Res, 23(3):869-880(2024) [pubmed]

submitter keyword: metaproteomic

sample preparation

Joelle Vinh
contact affiliation	Spectrométrie de Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249 ; 10 rue Vauquelin F-75005 Paris, France
contact email	joelle.vinh@espci.fr
lab head
Yann Verdier
contact affiliation	SMBP
contact email	yann.verdier@espci.fr
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/2024/05/PXD039581

PRIDE project URI

• PRIDE
  1. PXD039581
     1. Label: PRIDE project
     2. Name: ChipFilter: Microfluidic Based Comprehensive Sample Preparation Methodology for Metaproteomics