MassIVE MSV000095226

Complete Public PXD053601

Proteogenomic analysis of hiPSC cultures from a healthy donor

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Description

Proteogenomic analysis of three stem cell samples from a healthy donor. The cell lines used here are commercially available as induced pluripotent stem cells (iPSC) via retroviral reprogramming of skin fibroblasts isolated from the PGP1 donor from the Personal Genome Project (PGP) (Coriell, GM23338). hiPSC cultures were maintained as previously described [doi.org/10.1387/ijdb.230220lg]. Cell lysis, protein extraction, trypsin digestion, and peptide desalting were performed using the AccelerOme automated system from Thermo Fisher Scientific according to the manufacturer's instructions. Peptides were separated on a 110 cm micro-PAC HPLC column (Thermo Fisher Scientific) with a Vanquish Neo HPLC system (Thermo Fisher Scientific) coupled through a nano-electrospray source to a Tribrid Ascend mass spectrometer (Thermo Fisher Scientific) with a non-linear gradient of 1 - 50 % buffer B (0.1 % formic acid, 80 % acetonitrile) at a flow rate of 300 nL/min over 160min. The column temperature was kept at 50 C. Samples were acquired using a DDA MS2 data acquisition, where the Tribrid mass spectrometer was switching between a full scan (120 K resolution, Auto max. injection time, AGC target 100%), to a data-dependent (Top-20) MS/MS scans in the Orbitrap analyzer (15K resolution, 27 ms max. injection time, AGC target 400%). Isolation window was set to 1.4 (m/z), and normalized collision energy to 25. Precursors were filtered by charge state of 2-6 and multiple sequencing of peptides was minimized by excluding the selected peptide candidates for 60 s. Protein sequence database was generated by ProHap [doi.org/10.1101/2023.12.24.572591] using the phased genotype of the healthy donor, available from [https://my.pgp-hms.org/profile_public?hex=hu43860C]. [doi:10.25345/C50R9MG07] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: proteogenomics ; stem cells ; hiPSC ; iPSC ; DDA

Contact

Principal Investigators:
(in alphabetical order) 		Marc Vaudel, University of Bergen, Norway
Submitting User: jakub_vasicek
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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

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Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.