Protein elution profiles accompanying "A pan-plant protein complex map reveals deep conservation and novel assemblies"

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 counts of 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 counts of 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 reporting per-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 raw counts of peptide spectral matches (PSMs) for all observed orthogroups in one experiment
• Format: OrthogroupID,[Fractions]

[experiment_name].protcount.wide.gz

• Description: Elution profile of raw counts 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 |