DOI: 10.5281/zenodo.4451263
title: Protein elution profiles accompanying "A pan-plant protein complex map reveals deep conservation and novel assemblies"

description: Key to files <strong>Experiment_Order.csv</strong> Description: Meta details of each experiment. Format: experiment_name,ExperimentID_order,tissue,experiment_type,spec,ExperimentID <strong>Fraction_Details.csv</strong> Description: Meta details of each fraction Format:FractionID,frac_order,ExperimentID <strong>plant_virNOG_orthology.csv.gz</strong> Description: Conversion between orthogroup and protein IDs. Format:ID,ProteinID,spec <strong>orthogroup_annotation.csv.gz</strong> 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 <strong>panplant_tidy_elution_virNOG.csv.gz</strong> Description: Tidy (long format) table of counts of peptide spectral matches (PSMs) for all observed <strong>orthogroups</strong> for all experiments. Includes parts per million in each fraction. Format: ExperimentID,FractionID,ID,Total_PeptideCount,spec,ExperimentID_order,FractionID_order,abundance_ppm <strong>panplant_tidy_elution_protcount.csv.gz</strong> Description: Tidy (long format) table of counts of peptide spectral matches (PSMs) for all observed <strong>proteins</strong> for all experiments. Format: ExperimentID,FractionID,ProteinID,ProteinCount,spec,ExperimentID_order,FractionID_order <strong>panplant_wide_elution_virNOG.csv.gz</strong> Description: Table of concatenated elution profiles of raw counts of peptide spectral matches (PSMs) for all observed <strong>orthogroups</strong> Format: OrthogroupID,[Fractions] <strong>panplant_wide_elution_virNOG_annot.csv.gz</strong> Description: Table of concatenated elution profiles of raw counts of peptide spectral matches (PSMs) for all observed <strong>orthogroups</strong>, includes annotation columns. Format: OrthogroupID,[Annotations],[Fractions] <strong>panplant_wide_elution_expnorm.csv.gz</strong> Description: Table of concatenated elution profiles reporting per-fractionation experiment-normalized peptide spectral matches (PSMs) for all observed<strong> orthogroups</strong> Format: OrthogroupID,[Fractions] <strong>panplant_wide_elution_expnorm_annot.csv.gz</strong> Description: Table of concatenated elution profiles reporting per-fractionation experiment-normalized peptide spectral matches (PSMs) for all observed<strong> orthogroups</strong>, including columns with annotations Format: OrthogroupID,[Annotations],[Fractions] <strong>[experiment_name].virNOG.wide.gz</strong> Description: Elution profile of raw counts of peptide spectral matches (PSMs) for all observed<strong> orthogroups</strong> in one experiment Format: OrthogroupID,[Fractions] <strong>[experiment_name].protcount.wide.gz</strong> Description: Elution profile of raw counts of peptide spectral matches (PSMs) counts for all observed <strong>proteins </strong>in one experiment Format: ProteinID,[Fractions] <strong>[species]_specconcat.virNOG.wide.gz</strong> Description: Table of concatenated elution profiles of raw counts of peptide spectral matches (PSMs) for all observed <strong>orthogroups </strong>from a particular species. Only present for species with more than one experiment. Format: OrthogroupID,[Fractions] <strong>[species]_specconcat.protcount.wide.gz</strong> Description: Table of concatenated elution profiles of raw counts of peptide spectral matches (PSMs) for all observed <strong>proteins</strong> from a particular species. Only present for species with more than one experiment. Format: ProteinID,[Fractions] Species codes |Code | Species | Common name | Use |<br> |---|---|---|<br> | arath | Arabidopsis Thaliana | Arabidopsis | <br> | braol | Brassica oleracea | Broccoli |<br> | cansa | Cannabis sativa | hemp | <br> | cerri | Ceratopteris richardii | C-fern | <br> | chlre | Chlamydomonas reinhardtii | Chlamydomonas |<br> | chqui | Chenopodium quinoa | Quinoa | <br> | orysj | Oryza sativa var. japonica | Rice |<br> | selml | Selaginella moellendorffii | Selaginella | <br> | sollc | Solanum lycopersicum | Tomato | <br> | wheat | Triticum Aestivum | Wheat | <br> | soybn | Glycine max | Soybean | <br> | cocnu | Cocos nucifera | Coconut | | maize | MAIZE | maize |