Dataset Open Access

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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  <identifier identifierType="DOI">10.5281/zenodo.4451263</identifier>
  <creators>
    <creator>
      <creatorName>McWhite, Claire</creatorName>
      <givenName>Claire</givenName>
      <familyName>McWhite</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7346-3047</nameIdentifier>
      <affiliation>The University of Texas at Austin</affiliation>
    </creator>
    <creator>
      <creatorName>Papoulas, Ophelia</creatorName>
      <givenName>Ophelia</givenName>
      <familyName>Papoulas</familyName>
      <affiliation>The University of Texas at Austin</affiliation>
    </creator>
    <creator>
      <creatorName>Marcotte, Edward</creatorName>
      <givenName>Edward</givenName>
      <familyName>Marcotte</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-8808-180X</nameIdentifier>
      <affiliation>The University of Texas at Austin</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Protein elution profiles accompanying "A pan-plant protein complex map reveals deep conservation and novel assemblies"</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <dates>
    <date dateType="Issued">2020-02-13</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4451263</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3666941</relatedIdentifier>
  </relatedIdentifiers>
  <version>2.0</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Key to files&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Experiment_Order.csv&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Meta details of each experiment.&lt;/li&gt;
	&lt;li&gt;Format: experiment_name,ExperimentID_order,tissue,experiment_type,spec,ExperimentID&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;Fraction_Details.csv&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Meta details of each fraction&lt;/li&gt;
	&lt;li&gt;Format:FractionID,frac_order,ExperimentID&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;plant_virNOG_orthology.csv.gz&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Conversion between orthogroup and protein IDs.&lt;/li&gt;
	&lt;li&gt;Format:ID,ProteinID,spec&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;orthogroup_annotation.csv.gz&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Orthogroup annotations&lt;/li&gt;
	&lt;li&gt;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&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;panplant_tidy_elution_virNOG.csv.gz&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Tidy (long format) table of counts of peptide spectral matches (PSMs) for all observed &lt;strong&gt;orthogroups&lt;/strong&gt; for all experiments. Includes parts per million in each fraction.&amp;nbsp;&lt;/li&gt;
	&lt;li&gt;Format: ExperimentID,FractionID,ID,Total_PeptideCount,spec,ExperimentID_order,FractionID_order,abundance_ppm&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;panplant_tidy_elution_protcount.csv.gz&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Tidy (long format) table of counts of peptide spectral matches (PSMs) for all observed &lt;strong&gt;proteins&lt;/strong&gt; for all experiments.&amp;nbsp;&lt;/li&gt;
	&lt;li&gt;Format: ExperimentID,FractionID,ProteinID,ProteinCount,spec,ExperimentID_order,FractionID_order&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;panplant_wide_elution_virNOG.csv.gz&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
&lt;/ul&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Table of concatenated elution profiles of raw counts&amp;nbsp;of peptide spectral matches (PSMs) for all observed &lt;strong&gt;orthogroups&lt;/strong&gt;&lt;/li&gt;
	&lt;li&gt;Format: OrthogroupID,[Fractions]&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;panplant_wide_elution_virNOG_annot.csv.gz&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
&lt;/ul&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Table of concatenated elution profiles of raw counts&amp;nbsp;of peptide spectral matches (PSMs) for all observed &lt;strong&gt;orthogroups&lt;/strong&gt;, includes annotation columns.&lt;/li&gt;
	&lt;li&gt;Format: OrthogroupID,[Annotations],[Fractions]&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;panplant_wide_elution_expnorm.csv.gz&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
&lt;/ul&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Table of concatenated elution profiles reporting&amp;nbsp;per-fractionation experiment-normalized peptide spectral matches (PSMs) for all observed&lt;strong&gt; orthogroups&lt;/strong&gt;&lt;/li&gt;
	&lt;li&gt;Format: OrthogroupID,[Fractions]&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;panplant_wide_elution_expnorm_annot.csv.gz&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
&lt;/ul&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Table of concatenated elution profiles reporting per-fractionation experiment-normalized peptide spectral matches (PSMs) for all observed&lt;strong&gt; orthogroups&lt;/strong&gt;, including columns with annotations&lt;/li&gt;
	&lt;li&gt;Format: OrthogroupID,[Annotations],[Fractions]&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;[experiment_name].virNOG.wide.gz&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Elution profile of raw&amp;nbsp;counts of peptide spectral matches (PSMs)&amp;nbsp;for all observed&lt;strong&gt; orthogroups&lt;/strong&gt;&amp;nbsp;in one experiment&lt;/li&gt;
	&lt;li&gt;Format: OrthogroupID,[Fractions]&lt;/li&gt;
&lt;/ul&gt;

&lt;ul&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;[experiment_name].protcount.wide.gz&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Elution profile of raw&amp;nbsp;counts of peptide spectral matches (PSMs) counts for all observed &lt;strong&gt;proteins &lt;/strong&gt;in one experiment&lt;/li&gt;
	&lt;li&gt;Format: ProteinID,[Fractions]&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;[species]_specconcat.virNOG.wide.gz&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Table of concatenated elution profiles of raw counts of peptide spectral matches (PSMs)&amp;nbsp;for all observed &lt;strong&gt;orthogroups &lt;/strong&gt;from a particular species. Only present for species with more than one experiment.&amp;nbsp;&lt;/li&gt;
	&lt;li&gt;Format: OrthogroupID,[Fractions]&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;[species]_specconcat.protcount.wide.gz&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Description: Table of concatenated elution profiles of raw counts of peptide spectral matches (PSMs)&amp;nbsp;for all observed &lt;strong&gt;proteins&lt;/strong&gt; from a particular species. Only present for species with more than one experiment.&amp;nbsp;&lt;/li&gt;
	&lt;li&gt;Format: ProteinID,[Fractions]&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;ul&gt;
&lt;/ul&gt;

&lt;p&gt;Species codes&lt;/p&gt;

&lt;p&gt;|Code | Species | Common name &amp;nbsp; | Use |&lt;br&gt;
|---|---|---|&lt;br&gt;
| arath &amp;nbsp;| Arabidopsis Thaliana &amp;nbsp;| Arabidopsis &amp;nbsp;|&amp;nbsp;&lt;br&gt;
| braol &amp;nbsp;| Brassica oleracea &amp;nbsp;| Broccoli &amp;nbsp;|&lt;br&gt;
| cansa &amp;nbsp;| Cannabis sativa &amp;nbsp;| hemp &amp;nbsp;|&amp;nbsp;&lt;br&gt;
| cerri | Ceratopteris richardii | C-fern |&amp;nbsp;&lt;br&gt;
| chlre &amp;nbsp;| Chlamydomonas reinhardtii &amp;nbsp;| Chlamydomonas &amp;nbsp; |&lt;br&gt;
| chqui &amp;nbsp;| Chenopodium quinoa &amp;nbsp;| Quinoa &amp;nbsp;|&amp;nbsp;&lt;br&gt;
| orysj &amp;nbsp;| &amp;nbsp;Oryza sativa var. japonica | Rice &amp;nbsp;|&lt;br&gt;
| selml | Selaginella moellendorffii | Selaginella&amp;nbsp; |&amp;nbsp;&lt;br&gt;
| sollc &amp;nbsp;| Solanum &amp;nbsp;lycopersicum | Tomato &amp;nbsp;|&amp;nbsp;&lt;br&gt;
| wheat &amp;nbsp;| Triticum &amp;nbsp;Aestivum | Wheat &amp;nbsp;|&amp;nbsp;&lt;br&gt;
| soybn | Glycine max | Soybean |&amp;nbsp;&lt;br&gt;
| cocnu | Cocos nucifera | Coconut |&amp;nbsp;&lt;/p&gt;

&lt;p&gt;| maize | MAIZE | maize |&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;</description>
  </descriptions>
</resource>
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