PXD063969

PXD063969 is an original dataset announced via ProteomeXchange.

Title	Evaluating Protein Extraction Techniques for Elucidating Proteomic Changes in Yeast Deletion Strains
Description	Alterations in protein abundance profiles in yeast deletion strains are frequently utilized to gain insights into cellular functions and regulatory networks, most of which are conserved in higher eukaryotes. Here, we investigate the impact of protein extraction methodologies on proteomic analysis of S. cerevisiae, specifically, detergent-based lysis versus mechanical lysis with silica beads. We showcased this comparison by evaluating the proteomic profiles of wild-type and two yeast deletion strains, siz1Δ and nfi1Δ(siz2Δ), which are SUMO E3 ligases. Combining isobaric TMTpro-labeling with mass spectrometry using real-time search MS3, we profiled over 4,700 proteins, covering approximately 80% of the yeast proteome. Hierarchical clustering and principal component analyses revealed that the choice of protein extraction method influenced the proteomic data, overshadowing the genetic variances among these strains. Notably, the detergent-based lysis showed superior performance in extracting proteins, compared to mechanical lysis. Despite minimal proteomic alterations among strains, we observed consistent changes regardless of the lysis strategy in proteins such as Ino1, Rep1, Rep2, Snz1, and Fdh1 in both the two SUMO E3 ligases deletion strains, implying potential redundant mechanisms of control for these proteins. These data underscore the importance of method selection at each single step of sample preparation in proteomic studies and enhances our comprehension of cellular adaptations to genetic perturbations.
HostingRepository	PRIDE
AnnounceDate	2025-08-04
AnnouncementXML	Submission_2025-08-03_16:10:31.268.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	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-15 03:53:29	ID requested
⏵ 1	2025-08-03 16:10:32	announced

10.3390/proteomes13030028;

Rossio V, Paulo JA, Evaluating Protein Extraction Techniques for Elucidating Proteomic Changes in Yeast Deletion Strains. Proteomes, 13(3):(2025) [pubmed]

submitter keyword: protein extraction, bead-based lysis, SUMOylation, mass spectrometry, gene deletion,Yeast proteomics

Joao A. Paulo
contact affiliation	Department of Cell Biology Harvard Medical School Boston, MA 02115
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. PXD063969
     1. Label: PRIDE project
     2. Name: Evaluating Protein Extraction Techniques for Elucidating Proteomic Changes in Yeast Deletion Strains