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

Key to files <strong>Experiment_Order.csv</strong> Description: Meta details of each experiment. Format: experiment_name,ExperimentID_order,tissue,experiment_type,spec,ExperimentID <strong>Fraction_Details.csv</strong> Description: Meta details of each fraction Format:FractionID,frac_order,ExperimentID <strong>plant_virNOG_orthology.csv.gz</strong> Description: Conversion between orthogroup and protein IDs. Format:ID,ProteinID,spec <strong>orthogroup_annotation.csv.gz</strong> 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 <strong>panplant_tidy_elution_virNOG.csv.gz</strong> 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. Format: ExperimentID,FractionID,ID,Total_PeptideCount,spec,ExperimentID_order,FractionID_order,abundance_ppm <strong>panplant_tidy_elution_protcount.csv.gz</strong> Description: Tidy (long format) table of counts of peptide spectral matches (PSMs) for all observed <strong>proteins</strong> for all experiments. Format: ExperimentID,FractionID,ProteinID,ProteinCount,spec,ExperimentID_order,FractionID_order <strong>panplant_wide_elution_virNOG.csv.gz</strong> Description: Table of concatenated elution profiles of raw counts of peptide spectral matches (PSMs) for all observed <strong>orthogroups</strong> Format: OrthogroupID,[Fractions] <strong>panplant_wide_elution_virNOG_annot.csv.gz</strong> Description: Table of concatenated elution profiles of raw counts of peptide spectral matches (PSMs) for all observed <strong>orthogroups</strong>, includes annotation columns. Format: OrthogroupID,[Annotations],[Fractions] <strong>panplant_wide_elution_expnorm.csv.gz</strong> Description: Table of concatenated elution profiles reporting per-fractionation experiment-normalized peptide spectral matches (PSMs) for all observed<strong> orthogroups</strong> Format: OrthogroupID,[Fractions] <strong>panplant_wide_elution_expnorm_annot.csv.gz</strong> 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 Format: OrthogroupID,[Annotations],[Fractions] <strong>[experiment_name].virNOG.wide.gz</strong> Description: Elution profile of raw counts of peptide spectral matches (PSMs) for all observed<strong> orthogroups</strong> in one experiment Format: OrthogroupID,[Fractions] <strong>[experiment_name].protcount.wide.gz</strong> Description: Elution profile of raw counts of peptide spectral matches (PSMs) counts for all observed <strong>proteins </strong>in one experiment Format: ProteinID,[Fractions] <strong>[species]_specconcat.virNOG.wide.gz</strong> 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. Format: OrthogroupID,[Fractions] <strong>[species]_specconcat.protcount.wide.gz</strong> 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. Format: ProteinID,[Fractions] Species codes |Code | Species | Common name | Use |<br> |---|---|---|<br> | arath | Arabidopsis Thaliana | Arabidopsis | <br> | braol | Brassica oleracea | Broccoli |<br> | cansa | Cannabis sativa | hemp | <br> | cerri | Ceratopteris richardii | C-fern | <br> | chlre | Chlamydomonas reinhardtii | Chlamydomonas |<br> | chqui | Chenopodium quinoa | Quinoa | <br> | orysj | Oryza sativa var. japonica | Rice |<br> | selml | Selaginella moellendorffii | Selaginella | <br> | sollc | Solanum lycopersicum | Tomato | <br> | wheat | Triticum Aestivum | Wheat | <br> | soybn | Glycine max | Soybean | <br> | cocnu | Cocos nucifera | Coconut | | maize | MAIZE | maize |文件说明： 1. **Experiment_Order.csv**：记录每项实验的元数据，格式为：实验名称、实验ID排序号、组织、实验类型、物种、实验ID 2. **Fraction_Details.csv**：记录每个组分的元数据，格式为：组分ID、组分排序号、实验ID 3. **plant_virNOG_orthology.csv.gz**：直系同源组（orthogroup）与蛋白ID的对应关系表，格式为：ID、蛋白ID、物种 4. **orthogroup_annotation.csv.gz**：直系同源组注释表，格式为：ID、注释信息、拟南芥基因名、拟南芥条目、拟南芥条目名称、拟南芥蛋白名称、敲除事件、TAIR敲除事件、2012年Lloyd等研究的功能缺失突变、拟南芥功能、拟南芥杂项信息、通路、Unipathway、BioCyc、Reactome、BRENDA、KEGG通路、酶委员会编号、拟南芥质量、拟南芥蛋白名称、拟南芥基因本体（GO）、发育阶段、组织、TAIR、ARAPORT、水稻基因名、水稻条目、水稻条目名称、水稻蛋白名称、水稻敲除事件、水稻功能、水稻杂项信息 5. **panplant_tidy_elution_virNOG.csv.gz**：所有实验中所有观测到的直系同源组的肽段光谱匹配数（peptide spectral matches, PSM）的整洁长格式统计表，包含每个组分中的百万分比浓度（parts per million, ppm），格式为：实验ID、组分ID、直系同源组ID、总肽段计数、物种、实验ID排序号、组分ID排序号、丰度ppm 6. **panplant_tidy_elution_protcount.csv.gz**：所有实验中所有观测到的蛋白的肽段光谱匹配数的整洁长格式统计表，格式为：实验ID、组分ID、蛋白ID、蛋白计数、物种、实验ID排序号、组分ID排序号 7. **panplant_wide_elution_virNOG.csv.gz**：所有观测到的直系同源组的肽段光谱匹配数原始计数的整合洗脱谱表，格式为：直系同源组ID、[组分列] 8. **panplant_wide_elution_virNOG_annot.csv.gz**：所有观测到的直系同源组的肽段光谱匹配数原始计数的整合洗脱谱表，包含注释列，格式为：直系同源组ID、[注释列]、[组分列] 9. **panplant_wide_elution_expnorm.csv.gz**：所有观测到的直系同源组的、经单次分馏实验标准化后的肽段光谱匹配数的整合洗脱谱表，格式为：直系同源组ID、[组分列] 10. **panplant_wide_elution_expnorm_annot.csv.gz**：所有观测到的直系同源组的、经单次分馏实验标准化后的肽段光谱匹配数的整合洗脱谱表，包含注释列，格式为：直系同源组ID、[注释列]、[组分列] 11. **[experiment_name].virNOG.wide.gz**：单实验中所有观测到的直系同源组的肽段光谱匹配数原始计数的洗脱谱表，格式为：直系同源组ID、[组分列] 12. **[experiment_name].protcount.wide.gz**：单实验中所有观测到的蛋白的肽段光谱匹配数原始计数的洗脱谱表，格式为：蛋白ID、[组分列] 13. **[species]_specconcat.virNOG.wide.gz**：特定物种所有观测到的直系同源组的肽段光谱匹配数原始计数的整合洗脱谱表，仅当该物种包含多项实验时存在，格式为：直系同源组ID、[组分列] 14. **[species]_specconcat.protcount.wide.gz**：特定物种所有观测到的蛋白的肽段光谱匹配数原始计数的整合洗脱谱表，仅当该物种包含多项实验时存在，格式为：蛋白ID、[组分列] 物种代码对照表： | 代码 | 物种学名 | 通用名 | |---|---|---| | arath | *Arabidopsis thaliana* | 拟南芥 | | braol | *Brassica oleracea* | 西兰花 | | cansa | *Cannabis sativa* | 工业大麻 | | cerri | *Ceratopteris richardii* | C-蕨（水蕨） | | chlre | *Chlamydomonas reinhardtii* | 莱茵衣藻 | | chqui | *Chenopodium quinoa* | 藜麦 | | orysj | *Oryza sativa* var. *japonica* | 粳稻 | | selml | *Selaginella moellendorffii* | 卷柏 | | sollc | *Solanum lycopersicum* | 番茄 | | wheat | *Triticum aestivum* | 普通小麦 | | soybn | *Glycine max* | 大豆 | | cocnu | *Cocos nucifera* | 椰子 | | maize | MAIZE | 玉米 |