PXD004344

PXD004344 is an original dataset announced via ProteomeXchange.

Title	Histone modifications in Plasmodium falciparum at 0 hours post-invasion
Description	Synchronized Plasmodium falciparum-infected human blood cultures were harvested at seven time points along the asexual intra-erythrocytic parasite life cycle: 0 hours post-invasion, 6 hpi, 12 hpi, 18 hpi, 24 hpi, 30 hpi and 36 hpi. Plasmodium histones were extracted using the standard hydrochloric acid method and precipitated using trichloroacetic acid. Two biological replicates were digested with three enzymes of diverse specificities: endoproteinase LysC + trypsin (Ti), endoproteinase LysC + GluC (KCEC), and endoproteinase ArgC (RC). The resulting peptide mixtures were analyzed by Multidimensional Protein Identification Technology (MudPIT) coupled to high-resolution tandem mass spectrometry on an LTQ Orbitrap. RAW files were extracted into .ms2 file format using RawDistiller v. 1.0 (in-house developed software). After offline recalibration, the MS/MS spectra were first searched using SEQUEST v.27 (rev.9) with a peptide mass tolerance of 10 ppm and of +/- 0.5 amu for fragment ions. No enzyme specificity was imposed during the SEQUEST search against a protein database combining 5,439 non-redundant Plasmodium falciparum (PlasmoDB release 5.5) and 30,552 human proteins (NCBI 2008-03-04 release, as well as 162 usual 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 used for the SEQUEST searches, for a total search space of 72,306 amino acid sequences. To account for alkylation by CAM, 57.02146 Da were added statically to cysteine residues for all searches. We set up 44 searches to query for peptides containing various combinations of methylated lysines and arginines (+14.0157), oxidized methionines and hydroxylated lysines, prolines, aspartates, histidines, and tyrosines (+15.9949), formylated lysines and arginines (+27.9949), dimethylated lysines and arginines (+28.0314), trimethylated lysines (+42.0470), acetylated lysines, serines and threonines (+42.0106), crotonylated lysines (+68.0261), phosphorylated serines, threonines, and tyrosines (+79.9663), ubiquitinated lysines (+114.0429), as well as potentially N-terminally acetylated methionines, serines, alanines, and valines (+42.0106), and oxidized methionines (+58.0055). The maximum number of modified amino acids per differential modification in a peptide was limited to six. The MS/MS dataset was also searched using the same parameters with OMSSA to validate newly described PTMs.
HostingRepository	MassIVE
AnnounceDate	2016-06-16
AnnouncementXML	Submission_2016-06-16_05:57:24.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Laurence Florens
SpeciesList	scientific name: Plasmodium falciparum 3D7; NCBI TaxID: 36329; scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	N-acetyl-L-methionine; L-methionine sulfoxide; unknown modification: [M] [58.0055] N-acetyl-L-methionine sulfoxide; 5-hydroxy-L-lysine; N6-acetyl-L-lysine; N6-methyl-L-lysine; N6,N6-dimethyl-L-lysine; Trimethyl; N6-formyl-L-lysine; N6-crotonyl-L-lysine; ubiquitination signature dipeptidyl lysine; N5-methyl-L-arginine; symmetric dimethyl-L-arginine; formylated residue; O-phospho-L-serine; N-acetyl-L-serine; O-phospho-L-threonine; N-acetyl-L-threonine; O4'-phospho-L-tyrosine; 3'-hydroxylation of L-tyrosine to L-3',4'-dihydroxyphenylalanine; monohydroxylated proline; 3-hydroxy-L-histidine; 3-hydroxy-L-aspartic acid; N-acetyl-L-alanine; N-acetyl-L-valine; S-carboxamidomethyl-L-cysteine
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2016-06-16 05:57:21	ID requested
⏵ 1	2016-06-16 05:57:26	announced

Saraf A, Cervantes S, Bunnik EM, Ponts N, Sardiu ME, Chung DW, Prudhomme J, Varberg JM, Wen Z, Washburn MP, Florens L, Le Roch KG, Dynamic and Combinatorial Landscape of Histone Modifications during the Intraerythrocytic Developmental Cycle of the Malaria Parasite. J Proteome Res, 15(8):2787-801(2016) [pubmed]

submitter keyword: Histones, Post-translational Modifications, malaria parasite, intra-erythrocytic cycle, MudPIT

Laurence Florens
lab head
Laurence Florens
contact affiliation	Stowers Institute for Medical Research
contact email	laf@stowers.org
dataset submitter

MassIVE dataset URI

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