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PXD038457

PXD038457 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMudPIT analyses of the Plasmodium falciparum proteins pulled down by the kalihinol-analogue, MED6-189
DescriptionImmunoprecipitation 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%.
HostingRepositoryMassIVE
AnnounceDate2024-05-13
AnnouncementXMLSubmission_2024-05-13_11:14:07.357.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterStowers 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;
ModificationListL-methionine sulfoxide; S-carboxamidomethyl-L-cysteine
InstrumentLTQ
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-11-29 15:24:24ID requested
12024-05-13 11:14:07announced
Publication List
no publication
Keyword List
submitter keyword: Drug:Protein Interactions, affinity purification
Contact List
Laurence Florens
contact affiliationStowers Institute
contact emaillaf@stowers.org
lab head
Stowers Proteomics
contact affiliationStowers Institute for Med Res
contact emailproteomicslab@stowers.org
dataset submitter
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MassIVE dataset URI
Dataset FTP location
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