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

McWhite, Claire; Papoulas, Ophelia; Marcotte, Edward


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  <dc:creator>McWhite, Claire</dc:creator>
  <dc:creator>Papoulas, Ophelia</dc:creator>
  <dc:creator>Marcotte, Edward</dc:creator>
  <dc:date>2020-02-13</dc:date>
  <dc:description>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 | 

 </dc:description>
  <dc:identifier>https://zenodo.org/record/4451263</dc:identifier>
  <dc:identifier>10.5281/zenodo.4451263</dc:identifier>
  <dc:identifier>oai:zenodo.org:4451263</dc:identifier>
  <dc:relation>doi:10.5281/zenodo.3666941</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:title>Protein elution profiles accompanying "A pan-plant protein complex map reveals deep conservation and novel assemblies"</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>dataset</dc:type>
</oai_dc:dc>
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