PXD014582

PXD014582 is an original dataset announced via ProteomeXchange.

Title	Impact of protein search database on metaproteomics outcomes
Description	Unraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotype-genotype linkages. Despite its rapid development, this technology has faced many technical challenges that still hamper its potential power. How to maximize the number of protein identification, improve quality of protein annotation and provide reliable ecological interpretation, are questions of immediate urgency. In our study, we used a robust metaproteomic workflow combining two protein fractionation approaches (gel-based versus gel-free) and four protein search databases derived from the same metagenome to analyze the same seawater sample. The resulting eight metaproteomes provided different outcomes in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. The characterization and/or representativeness of numerous proteins from ecologically relevant taxa such as Pelagibacterales, Rhodobacterales and Synechococcales, as well as crucial environmental processes, such as nutrient uptake, nitrogen assimilation, light harvesting and oxidative stress response were found to be particularly affected by the methodology. Our results provide clear evidences that the use of different protein search databases significantly alters the biological conclusions in both gel-free and gel-based approaches. Our findings emphasize the importance of diversifying the experimental workflow for a comprehensive metaproteomic study.
HostingRepository	iProX
AnnounceDate	2019-07-12
AnnouncementXML	Submission_2020-08-10_21:44:25.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ageron
SpeciesList	scientific name: marine metagenome; NCBI TaxID: 408172;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-12 00:54:05	ID requested
1	2019-07-12 01:06:02	announced
⏵ 2	2020-08-10 21:44:27	announced	2020-08-11: Update publication information

G, é, ron A, Werner J, Wattiez R, Lebaron P, Matallana-Surget S, Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics. Front Microbiol, 10():2395(2019) [pubmed]

submitter keyword: Metaproteomics, Metagenomics, Bioinformatics, Mass Spectrometry, Microbial Ecology

S. Matallana-Surget
contact affiliation	University of Stirling
contact email	sabine.matallanasurget@stir.ac.uk
lab head
Ageron
contact affiliation	University of Stirling
contact email	a.f.geron@stir.ac.uk
dataset submitter

iProX dataset URI