PXD038457
PXD038457 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | MudPIT analyses of the Plasmodium falciparum proteins pulled down by the kalihinol-analogue, MED6-189 |
| Description | Immunoprecipitation followed by MudPIT mass spectrometry-- Mid- to late-stage asexual parasites were collected, purified, and were resuspended in 50mM Tris-HCl pH 7.5, 300mM NaCl, 0.5mM EDTA, 0.5mM EGTA, 2mM AEBSF, 0.5% Triton X-100, 20mM N-ethymaleimide and 1mM AEBSF and EDTA-free protease inhibitor cocktail (Roche). Post cell lysis solution was homogenized via sonication for 6-9 rounds at power level 3. The soluble extracts were centrifuged at 13,000g for 15min at 4C. The lysates were precleared with Dynabeads MyOne TM Streptavidin T1 (Invitrogen) for 1hr at 4C. 100uM of biotinylated kalihinol analogue (MED6-118) was added to each sample with the exception of DMSO added to a negative control and incubated for 1hr at 4C. Following drug incubation fresh Dynabeads MyOne TM Streptavidin T1 beads were added to each sample and incubated overnight at 4C. Dynabeads were used to precipitate biotinylated drug-protein complexes and washed three times with buffer (PBS, 0.05% Tween20). Proteins were eluted using 50mM Tris-HCl pH 6.7, 100mM DTT and 2% SDS. The eluent was subsequently precipitated in 20% TCA followed by cold acetone washes. The urea-denatured, reduced, alkylated, and digested proteins were analyzed by Multidimensional Protein Identification Technology (MudPIT) on a linear ion trap tandem mass spectrometer coupled to an Agilent 1100 series HPLC as described previously. Proteomics data processing and analysis-- Tandem mass (MS/MS) spectra were interpreted using ProluCID v.1.3.3 against a database consisting of 5527 non-redundant (NR) Plasmodium falciparum 3D7 proteins (PlasmoDB-42 release), 36661 NR human proteins (NCBI, 2018-03-30 release), 419 usual contaminants (human keratins, IgGs, and proteolytic enzymes). DTASelect v.1.9 and swallow v.0.0.1, an in-house developed software (https://github.com/tzw-wen/kite), were used to control FDRs at less than 1.2%. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-05-13 |
| AnnouncementXML | Submission_2024-05-13_11:14:07.357.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Stowers Proteomics |
| SpeciesList | scientific name: Plasmodium falciparum; common name: malaria parasite P. falciparum; NCBI TaxID: 5833; scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | L-methionine sulfoxide; S-carboxamidomethyl-L-cysteine |
| Instrument | LTQ |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2022-11-29 15:24:24 | ID requested | |
| ⏵ 1 | 2024-05-13 11:14:07 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Drug:Protein Interactions, affinity purification |
Contact List
| Laurence Florens | |
|---|---|
| contact affiliation | Stowers Institute |
| 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.ucsd.edu/v05/MSV000090812/ |
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