PXD044387

PXD044387 is an original dataset announced via ProteomeXchange.

Title	Comparison of the proteome and of the phosphoproteome of S. cerevisiae cells harvested with different strategies
Description	The budding yeast Saccharomyces cerevisiae is a powerful model system that is widely used to investigate many cellular processes. The harvesting of yeast cells is the first step in almost every experimental procedure. Here, yeast cells are isolated from their growth medium, collected, and used for successive experiments or analysis. The two most common methods to harvest S. cerevisiae are centrifugation and filtration. Understanding, if and how centrifugation and filtration affect yeast physiology is essential with respect to downstream data interpretation. Here, we profile and compare the proteomes and the phosphoproteomes, using isobaric label-based quantitative mass spectrometry, of three common methods used to harvest S. cerevisiae cells: low-speed centrifugation, high-speed centrifugation, and filtration. Our data suggest that while the proteome was stable across the tested conditions, hundreds of phosphorylation events were different between centrifugation and filtration. Our analysis shows that under our experimental conditions, filtration may cause both cell wall and osmotic stress at higher levels compared to centrifugation, and implying harvesting method-specific stresses. Thus, considering that the basal activation levels of specific stresses may differ under certain harvesting conditions is an important, but often overlooked aspect of experimental design.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:18:50.296.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-05 07:27:59	ID requested
1	2023-12-28 11:08:02	announced
⏵ 2	2024-10-22 06:18:52	announced	2024-10-22: Updated project metadata.

Rossio V, Paulo JA, Cells Harvested with Different Strategies. Proteomes, 11(4):(2023) [pubmed]

10.3390/proteomes11040028;

submitter keyword: yeast, proteome analysis, phosphoproteome analysis, stress,TMTpro

Joao A. Paulo
contact affiliation	Harvard Medical School Department of cell Biology Harvard Medical School Boston, MA, 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. PXD044387
     1. Label: PRIDE project
     2. Name: Comparison of the proteome and of the phosphoproteome of S. cerevisiae cells harvested with different strategies