PXD042292

PXD042292 is an original dataset announced via ProteomeXchange.

Title	Evaluation of Protein Extraction Methods to Improve Meta-Proteomics Analysis of Treated Wastewater Biofilms
Description	Metaproteomics can be used to study functionally active biofilm-based bacterial populations in reclaimed water distribution systems, which in turn result in bacterial regrowth that impacts the water quality. However, existing protein extraction methods have differences in their protein recovery and have not been evaluated for their efficacies in reclaimed water biofilm samples. In this study, we first evaluated six different protein extraction methods with diverse chemical and physical properties on a mixture of bacterial cell culture. Based on a weighting scores-based evaluation, the extraction protocols in order of decreasing performance are listed as B-PER > RIPA > PreOmics > SDS > AllPrep > Urea. The highest four optimal methods on cell culture were further tested against treated wastewater non-chlorinated and chlorinated effluent biofilms. In terms of protein yield, our findings showed that RIPA performed the best; however, the highest number of proteins were extracted from SDS and PreOmics. Furthermore, SDS and PreOmics worked best to rupture gram-positive and gram-negative bacterial cell walls. Considering the five evaluation factors, PreOmics obtained highest weighted score, indicating its potential effectiveness in extracting proteins from biofilms. This study provides the first insight into evaluating protein extraction methods to facilitate metaproteomics for complex reclaimed water matrices.
HostingRepository	PRIDE
AnnounceDate	2023-08-04
AnnouncementXML	Submission_2023-08-04_11:38:17.725.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD042292
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	FatimahAlmulhim
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Acinetobacter junii CIP 107470 = MTCC 11364; NCBI TaxID: 1217666; scientific name: Enterococcus faecalis (Streptococcus faecalis); NCBI TaxID: 1351; scientific name: bacterial mixed DNA library; NCBI TaxID: 1303873; scientific name: Staphylococcus aureus; NCBI TaxID: 1280;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-17 09:06:47	ID requested
⏵ 1	2023-08-04 11:38:18	announced

10.6019/PXD042292;

submitter keyword: biofilms

metaproteomic

methods evaluation

protein extraction

treated wastewater

Pei-YingHong
contact affiliation	Professor. Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
contact email	peiying.hong@kaust.edu.sa
lab head
FatimahAlmulhim
contact affiliation	PhD student
contact email	fatimah.almulhim@kaust.edu.sa
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/2023/08/PXD042292

PRIDE project URI

• PRIDE
  1. PXD042292
     1. Label: PRIDE project
     2. Name: Evaluation of Protein Extraction Methods to Improve Meta-Proteomics Analysis of Treated Wastewater Biofilms