⮝ Full datasets listing
PXD071777
PXD071777 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | C neoformans Rsp5 and trehalose biosynthesis proteomics, Alspaugh Lab |
| Description | Quantitative LC/MS/MS was performed on 250ng of sample using an EvoSep One UPLC coupled to a Thermo Orbitrap Astral high resolution accurate mass tandem mass spectrometer (Thermo). Briefly, each sample loaded EvoTip was eluted onto a 1.5 um EvoSep 150um ID x 8cm performance (EvoSep) column using the SPD60 gradient at 55C. Data collection on the Orbitrap Astral mass spectrometer was performed in a data-independent acquisition (DIA) mode of acquisition with a r=240,000 (m/z 200) full MS scan from m/z 380-980 in the OT with a target AGC value of 4e5 ions. Fixed DIA windows of 4 m/z from m/z 380 to 980 DIA MS/MS scans were acquired in the Astral with a target AGC value of 5e4 and max fill time of 6 ms. HCD collision energy setting of 27% was used for all MS2 scans. Raw data were imported into Spectronaut v20 (Biognosis) and MS/MS data was searched against a SwissProt C. neoformans H99 database (downloaded 2024). A library free Direct DIA+ approach within Spectronaut was used to perform the database searches set at a maximum 1% peptide false discovery rate based on q-value calculations. Database search parameters included fixed modification on Cys (carbamidomethyl) with variable modification on Met (oxidation). Full trypsin enzyme rules were used along with 10ppm mass tolerances on precursor ions and 20ppm on product ion. Peptide homology was addressed using razor rules in which a peptide matched to multiple different proteins was exclusively assigned to the protein with higher % sequence coverage. A MaxLFQ rollup strategy was deployed to roll up from the precursor level to the protein level. |
| HostingRepository | MassIVE |
| AnnounceDate | 2026-05-08 |
| AnnouncementXML | Submission_2026-05-08_08:42:36.364.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Erik Soderblom |
| SpeciesList | scientific name: Cryptococcus neoformans var. grubii H99; NCBI TaxID: 235443; |
| ModificationList | LRGG |
| Instrument | Orbitrap Astral |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2025-12-09 12:27:04 | ID requested | |
| ⏵ 1 | 2026-05-08 08:42:37 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: label free, GG, DatasetType:Proteomics |
Contact List
| Andrew Alspaugh | |
|---|---|
| contact affiliation | Duke University School of Medicine |
| contact email | andrew.alspaugh@duke.edu |
| lab head | |
| Erik Soderblom | |
| contact affiliation | Duke University |
| contact email | es114@duke.edu |
| 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/v11/MSV000100164/ |
