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Pulsed SILAC study of cell lines following PPIA knockdown

ABSTRACT: Mass spectrometry was performed with an Orbitrap Fusion Tribrid mass spectrometer (Thermo Scientific) interfaced with an UltiMate 3000 Binary RSLCnano System (Dionex). Proteome Discoverer v.1.4 (Thermo Scientific) with SEQUEST HT search engines was used for the spectra-preprocessing and HCD MS2 spectra were used for peptide identification and quantitation based on TMT reporter ions. Pulsed SILAC study of HEK293T cells and HeLa cells after knockdown (KD) of PPIA.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Andre Catic

PROVIDER: MSV000093125 | MassIVE | Mon Oct 16 16:49:00 BST 2023

SECONDARY ACCESSION(S): PXD046245

REPOSITORIES: MassIVE

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Publications

Cyclophilin A supports translation of intrinsically disordered proteins and affects haematopoietic stem cell ageing.

Maneix Laure L Iakova Polina P Lee Charles G CG Moree Shannon E SE Lu Xuan X Datar Gandhar K GK Hill Cedric T CT Spooner Eric E King Jordon C K JCK Sykes David B DB Saez Borja B Di Stefano Bruno B Chen Xi X Krause Daniela S DS Sahin Ergun E Tsai Francis T F FTF Goodell Margaret A MA Berk Bradford C BC Scadden David T DT Catic André A

Nature cell biology 20240329 4

Loss of protein function is a driving force of ageing. We have identified peptidyl-prolyl isomerase A (PPIA or cyclophilin A) as a dominant chaperone in haematopoietic stem and progenitor cells. Depletion of PPIA accelerates stem cell ageing. We found that proteins with intrinsically disordered regions (IDRs) are frequent PPIA substrates. IDRs facilitate interactions with other proteins or nucleic acids and can trigger liquid-liquid phase separation. Over 20% of PPIA substrates are involved in t ...[more]

PMID: 38553595

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Project description:Mass spectrometry was performed with an Orbitrap Fusion Tribrid mass spectrometer (Thermo Scientific) interfaced with an UltiMate 3000 Binary RSLCnano System (Dionex). Proteome Discoverer v.1.4 (Thermo Scientific) with SEQUEST HT search engines was used for the spectra-preprocessing and HCD MS2 spectra were used for peptide identification and quantitation based on TMT reporter ions. TMT isobaric comparison of Ppia heterozygous (het) versus knockout (KO) haematopoietic stem and progenitor cells. Het 1 is sample 126 and KO 1 is sample 131 of dataset UTH_2. Het 2 and KO 2 are samples 126 and 127 of UTH_4. Het 3 and KO 3 are samples 130 and 127 of dataset UTH_3.

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