MassIVE MSV000079229

Partial Public PXD004348

Histone modifications in Plasmodium falciparum at 24 hours post-invasion

Subscribe Comment Convert Spectra Reanalyze Spectra Add Reanalysis

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. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Histones ; Post-translational Modifications ; malaria parasite ; intra-erythrocytic cycle ; MudPIT

Contact

Principal Investigators:
(in alphabetical order) 		Laurence Florens
Submitting User: laflorens

Publications

Saraf A, Cervantes S, Bunnik EM, Ponts NP, Sardiu ME, Chung DD, Prudhomme J, Varberg J, Wen Z, Washburn MP, Florens LA, Le Roch KG.
Dynamic and combinatorial landscape of histone modifications during the intra-erythrocytic developmental cycle of the malaria parasite.
J. Proteome Res. Epub 2016 Jun 12.

Number of Files:
Total Size:
Spectra:
Subscribers:
 
Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
Browse Dataset Files
 
FTP Download Link (click to copy):

Species

Instrument

Modifications

- Dataset Reanalyses

+ Dataset History

Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.