February 13, 2020 Dataset Open Access

McWhite, Claire; Papoulas, Ophelia; Marcotte, Edward

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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.4451263", 
  "title": "Protein elution profiles accompanying \"A pan-plant protein complex map reveals deep conservation and novel assemblies\"", 
  "issued": {
    "date-parts": [
      [
        2020, 
        2, 
        13
      ]
    ]
  }, 
  "abstract": "<p>Key to files</p>\n\n<p><strong>Experiment_Order.csv</strong></p>\n\n<ul>\n\t<li>Description: Meta details of each experiment.</li>\n\t<li>Format: experiment_name,ExperimentID_order,tissue,experiment_type,spec,ExperimentID</li>\n</ul>\n\n<p><strong>Fraction_Details.csv</strong></p>\n\n<ul>\n\t<li>Description: Meta details of each fraction</li>\n\t<li>Format:FractionID,frac_order,ExperimentID</li>\n</ul>\n\n<p><strong>plant_virNOG_orthology.csv.gz</strong></p>\n\n<ul>\n\t<li>Description: Conversion between orthogroup and protein IDs.</li>\n\t<li>Format:ID,ProteinID,spec</li>\n</ul>\n\n<p><strong>orthogroup_annotation.csv.gz</strong></p>\n\n<ul>\n\t<li>Description: Orthogroup annotations</li>\n\t<li>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</li>\n</ul>\n\n<p><strong>panplant_tidy_elution_virNOG.csv.gz</strong></p>\n\n<ul>\n\t<li>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.&nbsp;</li>\n\t<li>Format: ExperimentID,FractionID,ID,Total_PeptideCount,spec,ExperimentID_order,FractionID_order,abundance_ppm</li>\n</ul>\n\n<p><strong>panplant_tidy_elution_protcount.csv.gz</strong></p>\n\n<ul>\n\t<li>Description: Tidy (long format) table of counts of peptide spectral matches (PSMs) for all observed <strong>proteins</strong> for all experiments.&nbsp;</li>\n\t<li>Format: ExperimentID,FractionID,ProteinID,ProteinCount,spec,ExperimentID_order,FractionID_order</li>\n</ul>\n\n<p><strong>panplant_wide_elution_virNOG.csv.gz</strong></p>\n\n<ul>\n</ul>\n\n<ul>\n\t<li>Description: Table of concatenated elution profiles of raw counts&nbsp;of peptide spectral matches (PSMs) for all observed <strong>orthogroups</strong></li>\n\t<li>Format: OrthogroupID,[Fractions]</li>\n</ul>\n\n<p><strong>panplant_wide_elution_virNOG_annot.csv.gz</strong></p>\n\n<ul>\n</ul>\n\n<ul>\n\t<li>Description: Table of concatenated elution profiles of raw counts&nbsp;of peptide spectral matches (PSMs) for all observed <strong>orthogroups</strong>, includes annotation columns.</li>\n\t<li>Format: OrthogroupID,[Annotations],[Fractions]</li>\n</ul>\n\n<p><strong>panplant_wide_elution_expnorm.csv.gz</strong></p>\n\n<ul>\n</ul>\n\n<ul>\n\t<li>Description: Table of concatenated elution profiles reporting&nbsp;per-fractionation experiment-normalized peptide spectral matches (PSMs) for all observed<strong> orthogroups</strong></li>\n\t<li>Format: OrthogroupID,[Fractions]</li>\n</ul>\n\n<p><strong>panplant_wide_elution_expnorm_annot.csv.gz</strong></p>\n\n<ul>\n</ul>\n\n<ul>\n\t<li>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</li>\n\t<li>Format: OrthogroupID,[Annotations],[Fractions]</li>\n</ul>\n\n<p><strong>[experiment_name].virNOG.wide.gz</strong></p>\n\n<ul>\n\t<li>Description: Elution profile of raw&nbsp;counts of peptide spectral matches (PSMs)&nbsp;for all observed<strong> orthogroups</strong>&nbsp;in one experiment</li>\n\t<li>Format: OrthogroupID,[Fractions]</li>\n</ul>\n\n<ul>\n</ul>\n\n<p><strong>[experiment_name].protcount.wide.gz</strong></p>\n\n<ul>\n\t<li>Description: Elution profile of raw&nbsp;counts of peptide spectral matches (PSMs) counts for all observed <strong>proteins </strong>in one experiment</li>\n\t<li>Format: ProteinID,[Fractions]</li>\n</ul>\n\n<p><strong>[species]_specconcat.virNOG.wide.gz</strong></p>\n\n<ul>\n\t<li>Description: Table of concatenated elution profiles of raw counts of peptide spectral matches (PSMs)&nbsp;for all observed <strong>orthogroups </strong>from a particular species. Only present for species with more than one experiment.&nbsp;</li>\n\t<li>Format: OrthogroupID,[Fractions]</li>\n</ul>\n\n<p><strong>[species]_specconcat.protcount.wide.gz</strong></p>\n\n<ul>\n\t<li>Description: Table of concatenated elution profiles of raw counts of peptide spectral matches (PSMs)&nbsp;for all observed <strong>proteins</strong> from a particular species. Only present for species with more than one experiment.&nbsp;</li>\n\t<li>Format: ProteinID,[Fractions]</li>\n</ul>\n\n<p>&nbsp;</p>\n\n<ul>\n</ul>\n\n<p>Species codes</p>\n\n<p>|Code | Species | Common name &nbsp; | Use |<br>\n|---|---|---|<br>\n| arath &nbsp;| Arabidopsis Thaliana &nbsp;| Arabidopsis &nbsp;|&nbsp;<br>\n| braol &nbsp;| Brassica oleracea &nbsp;| Broccoli &nbsp;|<br>\n| cansa &nbsp;| Cannabis sativa &nbsp;| hemp &nbsp;|&nbsp;<br>\n| cerri | Ceratopteris richardii | C-fern |&nbsp;<br>\n| chlre &nbsp;| Chlamydomonas reinhardtii &nbsp;| Chlamydomonas &nbsp; |<br>\n| chqui &nbsp;| Chenopodium quinoa &nbsp;| Quinoa &nbsp;|&nbsp;<br>\n| orysj &nbsp;| &nbsp;Oryza sativa var. japonica | Rice &nbsp;|<br>\n| selml | Selaginella moellendorffii | Selaginella&nbsp; |&nbsp;<br>\n| sollc &nbsp;| Solanum &nbsp;lycopersicum | Tomato &nbsp;|&nbsp;<br>\n| wheat &nbsp;| Triticum &nbsp;Aestivum | Wheat &nbsp;|&nbsp;<br>\n| soybn | Glycine max | Soybean |&nbsp;<br>\n| cocnu | Cocos nucifera | Coconut |&nbsp;</p>\n\n<p>| maize | MAIZE | maize |&nbsp;</p>\n\n<p>&nbsp;</p>", 
  "author": [
    {
      "family": "McWhite, Claire"
    }, 
    {
      "family": "Papoulas, Ophelia"
    }, 
    {
      "family": "Marcotte, Edward"
    }
  ], 
  "version": "2.0", 
  "type": "dataset", 
  "id": "4451263"
}