PXD026759
PXD026759 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Secretome of corneal stroma stem cells promotes scarless corneal wound healing by modulating inflammation and sensory nerve regeneration |
| Description | TCA-precipitated proteins were urea-denatured, reduced, alkylated and digested with endoproteinase Lys-C followed by modified trypsin. Peptide mixtures were loaded onto 250 um fused silica microcapillary columns packed with strong cation exchange resin and 5-um C18 reverse phase, and then connected to a 100 um fused silica microcapillary column packed with 5-um C18 reverse phase. Loaded microcapillary columns were placed in-line with a Quaternary Agilent 1100 series HPLC pump and a LTQ Orbitrap Elite mass spectrometer equipped with a nano-LC electrospray ionization source. Fully automated 10-step MudPIT runs were carried out on the electrosprayed peptides. Tandem mass (MS/MS) spectra were interpreted using ProluCID against a database consisting of 79096 nonredundant Human proteins (NCBI, 2016-06-10 release), 193 usual contaminants. To estimate false discovery rates (FDR)s, the amino acid sequence of each non-redundant proteinentry was randomized to generate a virtual library. This resulted in a total library of 158578 non-redundant sequences against which the spectra were matched. All cysteines were considered as fully carboxamidomethylated, while methionine oxidation was searched as a differential modification. DTASelect and swallow, an in-house developed software, were used to filter ProLuCID search results at given FDRs at the spectrum, peptide, and protein levels. Here all controlled FDRs were less than 5%. All 4 data sets were contrasted against their merged data set, respectively, using Contrast v 1.9 and in house developed sandmartin v0.0.1. Our in-house developed software, NSAF7 v0.0.1, was used to generate spectral count-based label free quantitation results. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-04-03 |
| AnnouncementXML | Submission_2025-04-03_09:03:03.224.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Stowers Proteomics |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | L-methionine sulfoxide; iodoacetamide - site C |
| Instrument | LTQ Orbitrap Elite |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2021-06-17 16:32:42 | ID requested | |
| ⏵ 1 | 2025-04-03 09:03:03 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: secretome |
Contact List
| Laurence Florens | |
|---|---|
| contact affiliation | The Stowers Institute for Medical Research |
| contact email | laf@stowers.org |
| lab head | |
| Stowers Proteomics | |
| contact affiliation | Stowers Institute for Med Res |
| contact email | proteomicslab@stowers.org |
| 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-ftp.ucsd.edu/v03/MSV000087651/ |
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