Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum

Additional file 1:

Detailed protocols for all experimental and bioinformatic analyses performed in this study (1a to 1f).

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Additional file 2:

Summary table of tryptic peptides measured by MudPIT and Spearman rank correlations between replicates.

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Additional file 3:

Raw SEQUEST output data for peptide tandem mass spectra and proteins detected in ring stage parasites.

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Additional file 4:

Raw SEQUEST output data for peptide tandem mass spectra and proteins detected in trophozoites.

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Additional file 5:

Raw SEQUEST output data for peptide tandem mass spectra and proteins detected in schizonts.

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Additional file 6:

Extensive summary table for all proteins detected in this study.

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Additional file 7:

Enrichment analyses for KEGG pathways and GO terms in proteins found only in the combined nuclear or cytoplasmic fractions.

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Additional file 8:

P. falciparum protein localizations derived from published sources through homology.

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Additional file 9:

Proteins removed from the bioinformatically filtered nuclear proteome (worksheet A). Proteins re-added to the nuclear proteome after they were removed by bioinformatic filtering (worksheet B). Proteins with recently added signal peptide annotation (worksheet C). Proteins with recently removed signal peptide annotation (worksheet D).

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Additional file 10:

Extensive summary table for all proteins in the core nuclear proteome.

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Additional file 11:

List of proteins tagged and localized in this study.

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Additional file 12:

Detailed IFA localization of NuProCs 1 to 22 during the IDC.

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Additional file 13:

Detailed IFA localization of n-NuProCs 1 to 6 during the IDC.

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Additional file 14:

Multiple sequence alignments in graphical format of: (1) the ACDC domains in apicomplexan proteins; (2) the apicomplexan proteins encoding the partial CSTF domain; (3) the P. falciparum proteins encoding the extended ELM2 domain; (4) the P. falciparum proteins encoding the MYND domain.

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Additional file 15:

A multiple sequence alignment of the apicomplexan proteins encoding the ACDC domain is shown in aligned FASTA format. This file can be viewed using JalView [135].

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Additional file 16:

HMM used to query the P. falciparum and other alveolate whole proteomes to detect ACDC domains, in stockholm format. Note that this is not an HMM built from all putative ACDC domains, but simply an intermediate file used during the methodology of this publication. This file can be viewed using LogoMat-P [136].

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Additional file 17:

A multiple sequence alignment of the apicomplexan proteins encoding the partial CSTF domain in aligned FASTA format. This file can be viewed using JalView [135].

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Additional file 18:

A multiple sequence alignment of the apicomplexan proteins encoding the extended ELM2 domain in aligned FASTA format. This file can be viewed using JalView [135].

Format: FASTA Size: 9KB Download file

Additional file 19:

A multiple sequence alignment of the apicomplexan proteins encoding the MYND domain in aligned FASTA format. This file can be viewed using JalView [135].

Format: FASTA Size: 9KB Download file

Additional file 20:

Pairwise sequence alignment of the two putative FG-repeat proteins PFI0250c and PF14_0442.

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Additional file 21:

PCR and western blot analysis to confirm C-terminal tagging of endogenous PF14_0442 by 3' replacement.

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Additional file 22:

cNLSs prediction in P. falciparum nuclear proteins.

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Additional file 23:

mRNA expression profiles and maximal hour of mRNA expression of proteins found stage-specifically in the nuclear proteome.

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Additional file 24:

List of stage-specifically detected TFs.

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Additional file 25:

Summary table for lineage-specific proteins in the core nuclear proteome.

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Additional file 26:

List of all primers used in this study.

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