PXD053855

PXD053855 is an original dataset announced via ProteomeXchange.

Title	High-throughput cell-based proteomics perturbation: Buffer Optimization
Description	We have developed a high-throughput (HTP) cell-based workflow for the accurate quantification of proteins from approximately 100 samples per day. This bottom-up proteomics workflow automates the processing of cells grown in 96-well plates for liquid-chromatography mass spectrometry (LC-MS) analysis. The HTP system leverages the LE220-plus focused-ultrasonicator system (Covaris) for cell lysis and solubilization in tandem with the Biomek i7 automated liquid handling workstation (Beckman) for subsequent peptide processing prior to LC-MS. AC16 human cardiomyocytes were cultured in a 96-well plate under optimized conditions that was compatible with downstream HTP cell-based assay investigation. Sonication parameters and solubilization buffers were evaluated. An average protein concentration of 0.5 microg/microl was obtained from approximately 38,000 cells and optimal cell lysis was observed in 5 % SDS. SDS-based extraction resulted in more than 70,000 peptides to identify 4,300 proteins, with 75 % of proteins measured at an average coefficient of variation (CV) under 25%. Our HTP system was also adapted to detect proteins from low peptide loads or with short LC-MS acquisition gradients. Our HTP protocol was further evaluated in a cell model of cardiac ischemic reperfusion. Proteomic analysis of differentially expressed proteins (DEPs) demonstrated significant down-regulation in hypoxic state and an influx in reperfused condition, with most upregulated proteins involved in lipid and metabolic metabolism, the main drivers after hypoxic cellular injury. The developed HTP pipeline can be applied to both label free and stable isotope-labeling as well as investigating important key regulators in major cell-based assays, including post-translational modifications. Furthermore, drug targets and cellular perturbations could be rapidly investigated.
HostingRepository	MassIVE
AnnounceDate	2025-02-28
AnnouncementXML	Submission_2025-02-28_15:34:57.120.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Niveda Sundararaman
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-10 11:12:04	ID requested
⏵ 1	2025-02-28 15:34:57	announced

no publication

submitter keyword: Precision medicine , high-throughput, cell-based assay, protein extraction workflow, detergent-free, perturbation, mitochondria, ischemic hypoxiaand reperfusion

Jennifer Van Eyk
contact affiliation	Cedars Sinai Medical Center
contact email	jennifer.vaneyk@cshs.org
lab head
Niveda Sundararaman
contact affiliation	Cedars SInai Medical Center
contact email	Niveda.Sundararaman@cshs.org
dataset submitter

MassIVE dataset URI

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