Dataset Open Access
McWhite, Claire;
Papoulas, Ophelia;
Marcotte, Edward
{ "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. </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. </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 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 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 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 counts of peptide spectral matches (PSMs) for all observed<strong> orthogroups</strong> 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 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) for all observed <strong>orthogroups </strong>from a particular species. Only present for species with more than one experiment. </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) for all observed <strong>proteins</strong> from a particular species. Only present for species with more than one experiment. </li>\n\t<li>Format: ProteinID,[Fractions]</li>\n</ul>\n\n<p> </p>\n\n<ul>\n</ul>\n\n<p>Species codes</p>\n\n<p>|Code | Species | Common name | Use |<br>\n|---|---|---|<br>\n| arath | Arabidopsis Thaliana | Arabidopsis | <br>\n| braol | Brassica oleracea | Broccoli |<br>\n| cansa | Cannabis sativa | hemp | <br>\n| cerri | Ceratopteris richardii | C-fern | <br>\n| chlre | Chlamydomonas reinhardtii | Chlamydomonas |<br>\n| chqui | Chenopodium quinoa | Quinoa | <br>\n| orysj | Oryza sativa var. japonica | Rice |<br>\n| selml | Selaginella moellendorffii | Selaginella | <br>\n| sollc | Solanum lycopersicum | Tomato | <br>\n| wheat | Triticum Aestivum | Wheat | <br>\n| soybn | Glycine max | Soybean | <br>\n| cocnu | Cocos nucifera | Coconut | </p>\n\n<p>| maize | MAIZE | maize | </p>\n\n<p> </p>", "author": [ { "family": "McWhite, Claire" }, { "family": "Papoulas, Ophelia" }, { "family": "Marcotte, Edward" } ], "version": "2.0", "type": "dataset", "id": "4451263" }
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