PXD042292 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-05-17 09:06:47 | ID requested | |
⏵ 1 | 2023-08-04 11:38:18 | announced | |
Publication List
Keyword List
submitter keyword: biofilms |
metaproteomic |
methods evaluation |
protein extraction |
treated wastewater |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD042292
- Label: PRIDE project
- Name: Evaluation of Protein Extraction Methods to Improve Meta-Proteomics Analysis of Treated Wastewater Biofilms