PXD053601-1
PXD053601 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Proteogenomic analysis of hiPSC cultures from a healthy donor |
| 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]. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-07-03 |
| AnnouncementXML | Submission_2024-07-03_05:30:56.909.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Jakub Vasicek |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Carbamidomethyl |
| Instrument | Orbitrap Ascend |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-07-03 05:07:49 | ID requested | |
| ⏵ 1 | 2024-07-03 05:30:57 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: proteogenomics, stem cells, hiPSC, iPSC, DDA |
Contact List
| Marc Vaudel | |
|---|---|
| contact affiliation | University of Bergen |
| contact email | marc.vaudel@uib.no |
| lab head | |
| Jakub Vasicek | |
| contact affiliation | University of Bergen |
| contact email | jakub.vasicek@uib.no |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/v08/MSV000095226/ |
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