PXD020816

PXD020816 is an original dataset announced via ProteomeXchange.

Title	Growth media-based proteome remodeling of three microorganisms using sample multiplexing
Description	The choice of growth media is a very important consideration of any cell-based proteomics experiment. Alterations thereof may result in differences in basal proteomes simply due to disparities in the metabolite composition of the media. We investigate the effect of growth media on the proteomes of three microorganisms, specifically E. coli, S. cerevisiae, and S. pombe, using tandem mass tag (TMT)-based quantitative proteomics. We compared the protein abundance profiles of these microorganisms propagated in two distinct growth media that are commonly used for the respective organism. Our sample preparation strategy included SP3 bead-assisted protein isolation and digestion. In addition, we assembled a replicate set of samples in which we altered the proteolytic digestion from sequential treatment with LysC and trypsin to only LysC. Despite differences in peptides identified and a drop in quantified proteins, the results were similar between the two datasets for all three microorganisms. Approximately 10% of the respective microbial proteomes were significantly altered in each dataset. As expected, gene ontology analysis revealed that the majority of differentially expressed proteins are implicated in metabolism. We emphasize further the importance of growth media selection and the potential consequences thereof.
HostingRepository	PRIDE
AnnounceDate	2021-05-11
AnnouncementXML	Submission_2021-05-11_06:34:20.915.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Schizosaccharomyces pombe 927; NCBI TaxID: 1264690; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-09 23:34:17	ID requested
⏵ 1	2021-05-11 06:34:21	announced

Navarrete-Perea J, Gygi SP, Paulo JA, Growth media selection alters the proteome profiles of three model microorganisms. J Proteomics, 231():104006(2021) [pubmed]

submitter keyword: SPS-MS3, Multi-Notch, TMT, Lumos, microorganism

Joao A. Paulo
contact affiliation	Department of Cell Biology, Harvard Medical School, USA
contact email	joao_paulo@post.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD020816
     1. Label: PRIDE project
     2. Name: Growth media-based proteome remodeling of three microorganisms using sample multiplexing