⮝ Full datasets listing
PXD074785-1
PXD074785 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | The human parasite, Toxoplasma gondii, is paralyzed without two components of the apical polar ring |
| Description | Protein samples were processed for MudPIT as described in [61]. MS/MS spectra were first searched using ProLuCID v. 1.3.3 with a mass tolerance of 10 ppm for peptide and fragment ions. Trypsin specificity was imposed on both ends of candidate peptides during the search against a protein database containing 48080 non-redundant (NR) human proteins (combining entries from GCF_000001405.40_GRCh38.p14 and GCF_009914755.1_T2T-CHM13v2.0) and 8450 Toxoplasma gondii NR proteins (TGGT1 entries from ToxoDB-53), as well as 428 common contaminants such as human keratins, IgGs and proteolytic enzymes. To estimate false discovery rates (FDR), each protein sequence was randomized (keeping the same amino acid composition and length) and the resulting "shuffled" sequences were added to the database with mEmeraldFP-APR2 for a total search space of 113917 amino acid sequences. Combining all replicate runs, proteins had to be detected by at least 2 peptides and/or 2 spectral counts. Proteins that were subsets of others were removed using the parsimony option in DTASelect v. 1.9 on the proteins detected after merging all runs. Proteins that were identified by the same set of peptides (including at least one peptide unique to such protein group to distinguish between isoforms) were grouped together, and one accession number was arbitrarily considered as representative of each protein group. NSAF7 v. 0.0.1 (https://github.com/tzw-wen/kite/tree/master/ windowsapp/NSAF7x64), was used to create the final reports on all detected peptides and nonredundant proteins identified across the different runs and to calculate quantitative label-free distributed normalized spectral abundance factor (dNSAF) values for all detected protein/ protein groups. |
| HostingRepository | MassIVE |
| AnnounceDate | 2026-06-16 |
| AnnouncementXML | Submission_2026-06-16_07:31:29.708.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Stowers Proteomics |
| SpeciesList | scientific name: Toxoplasma gondii; NCBI TaxID: 5811; |
| ModificationList | iodoacetamide - site C; L-methionine sulfoxide |
| Instrument | LTQ Orbitrap Velos |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2026-02-24 14:15:50 | ID requested | |
| ⏵ 1 | 2026-06-16 07:31:30 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: MudPIT APR2, DatasetType:Proteomics |
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/v12/MSV000100958/ |
