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PXD000070

PXD000070 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlePlasmodium falciparum schizont phosphoproteome
DescriptionPlasmodium falciparum schizont proteins were extracted using SDS, digested with trypsin and phosphopeptides were enriched using IMAC. Phosphopeptides were analysed using either decision tree or data dependent neutral loss triggered ETD acquisition. All raw MS data files were processed and converted into MGF file format using Proteome Discoverer 1.1 (Thermo Scientific). A precursor filter of 600-10000 Da and a non-fragment filter were applied to ETD spectra to remove un-reacted precursor peaks, charge reduced precursor peaks, neutral losses from charge reduced precursors and FT Overtones using default settings. All ion trap spectra with less than 15 fragmentation peaks were removed and a signal to noise filter of 3 was applied to all spectra. All datasets were searched using Mascot v2.2 (Matrix Science) against a combined Human (IPI, 2010) and Plasmodium falciparum (GeneDB) sequence database (79,637 sequences) using the following search parameters: trypsin with a maximum of 3 missed cleavages, 10 ppm for MS mass tolerance, 0.5 Da for MS/MS mass tolerance, with Acetyl (Protein N-term), Oxidation (M), Deamidated (NQ), Carbamidomethyl (C) and Phospho ST set as variable modifications. ETD spectra were searched using c, z and y ion series and CID data was searched using b and y ion series.  All searches used Mascot’s automated decoy database searching.
HostingRepositoryPRIDE
AnnounceDate2014-07-24
AnnouncementXMLSubmission_2014-07-24_03:46:40.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD000070
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterMark Collins
SpeciesList scientific name: Plasmodium falciparum (isolate 3D7); NCBI TaxID: 36329;
ModificationListdeamidated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; phosphorylated residue
InstrumentLTQ Orbitrap Velos; instrument model: LTQ Orbitrap Velos ETD
Dataset History
RevisionDatetimeStatusChangeLog Entry
02012-11-15 01:15:27ID requested
12014-04-24 12:39:45announced
22014-07-24 03:46:41announcedUpdated project metadata.
Publication List
Collins MO, Wright JC, Jones M, Rayner JC, Choudhary JS, Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation. J Proteomics, 103(100):1-14(2014) [pubmed]
Keyword List
curator keyword: Technical
submitter keyword: Plasmodium falciparum, phosphoproteome, CID, ETD
Contact List
Mark Collins
contact affiliationTeam 32
contact emailmoc@sanger.ac.uk
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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