Protein elution profiles accompanying "A pan-plant protein complex map reveals deep conservation and novel assemblies"
DOI10.5281/zenodo.4451263Zenodo4451263MaRDI QIDQ6686169FDOQ6686169
Dataset published at Zenodo repository.
Ophelia Papoulas, Edward Marcotte, Claire D McWhite
Publication date: 13 February 2020
Copyright license: Creative Commons Attribution 4.0 International
Key to files Experiment_Order.csv Description: Meta details of each experiment. Format: experiment_name,ExperimentID_order,tissue,experiment_type,spec,ExperimentID Fraction_Details.csv Description: Meta details of each fraction Format:FractionID,frac_order,ExperimentID plant_virNOG_orthology.csv.gz Description: Conversion between orthogroup and protein IDs. Format:ID,ProteinID,spec orthogroup_annotation.csv.gz Description: Orthogroup annotations Format:ID,Annotation,arath_genenames,arath_Entries,arath_Entry_names,arath_Protein_names,disruptions,tair_disruptions,lloyd2012_LOFs,arath_functions,arath_misc,pathway,unipathway,BioCyc,Reactome,BRENDA,kegg_pws,ec,arath_masses,arath_protein_names,arath_GO,devstages,tissues,tair,araport,orysj_genenames,orysj_Entries,orysj_Entry_names,orysj_Protein_names,orysj_disruptions,orysj_functions,orysj_misc panplant_tidy_elution_virNOG.csv.gz Description: Tidy (long format) table of counts of peptide spectral matches (PSMs) for all observed orthogroups for all experiments. Includes parts per million in each fraction. Format: ExperimentID,FractionID,ID,Total_PeptideCount,spec,ExperimentID_order,FractionID_order,abundance_ppm panplant_tidy_elution_protcount.csv.gz Description: Tidy (long format) table of counts of peptide spectral matches (PSMs) for all observed proteins for all experiments. Format: ExperimentID,FractionID,ProteinID,ProteinCount,spec,ExperimentID_order,FractionID_order panplant_wide_elution_virNOG.csv.gz Description: Table of concatenated elution profiles of raw countsof peptide spectral matches (PSMs) for all observed orthogroups Format: OrthogroupID,[Fractions] panplant_wide_elution_virNOG_annot.csv.gz Description: Table of concatenated elution profiles of raw countsof peptide spectral matches (PSMs) for all observed orthogroups, includes annotation columns. Format: OrthogroupID,[Annotations],[Fractions] panplant_wide_elution_expnorm.csv.gz Description: Table of concatenated elution profiles reportingper-fractionation experiment-normalized peptide spectral matches (PSMs) for all observed orthogroups Format: OrthogroupID,[Fractions] panplant_wide_elution_expnorm_annot.csv.gz Description: Table of concatenated elution profiles reporting per-fractionation experiment-normalized peptide spectral matches (PSMs) for all observed orthogroups, including columns with annotations Format: OrthogroupID,[Annotations],[Fractions] [experiment_name].virNOG.wide.gz Description: Elution profile of rawcounts of peptide spectral matches (PSMs)for all observed orthogroupsin one experiment Format: OrthogroupID,[Fractions] [experiment_name].protcount.wide.gz Description: Elution profile of rawcounts of peptide spectral matches (PSMs) counts for all observed proteins in one experiment Format: ProteinID,[Fractions] [species]_specconcat.virNOG.wide.gz Description: Table of concatenated elution profiles of raw counts of peptide spectral matches (PSMs)for all observed orthogroups from a particular species. Only present for species with more than one experiment. Format: OrthogroupID,[Fractions] [species]_specconcat.protcount.wide.gz Description: Table of concatenated elution profiles of raw counts of peptide spectral matches (PSMs)for all observed proteins from a particular species. Only present for species with more than one experiment. Format: ProteinID,[Fractions] Species codes |Code | Species | Common name | Use | |---|---|---| | arath | Arabidopsis Thaliana | Arabidopsis | | braol | Brassica oleracea | Broccoli | | cansa | Cannabis sativa | hemp | | cerri | Ceratopteris richardii | C-fern | | chlre | Chlamydomonas reinhardtii | Chlamydomonas | | chqui | Chenopodium quinoa | Quinoa | | orysj | Oryza sativa var. japonica | Rice | | selml | Selaginella moellendorffii | Selaginella | | sollc | Solanum lycopersicum | Tomato | | wheat | Triticum Aestivum | Wheat | | soybn | Glycine max | Soybean | | cocnu | Cocos nucifera | Coconut | | maize | MAIZE | maize |
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