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

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 | 

 

Files (121.4 MB)
Name Size
arath_Arabidopsis_sprouts_WWC_2017.protcount.wide.gz
md5:80ba5c2a9d4d3bff17fbdb5c69ec9377
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arath_Arabidopsis_sprouts_WWC_2017_virNOG.wide.gz
md5:ee81c95e81ba7c23cab068cd2a417658
159.4 kB Download
arath_At_Col_0_indark_201505.protcount.wide.gz
md5:0425e03c52a2cf058a24a1bad4cc78dc
189.7 kB Download
arath_At_Col_0_indark_201505_virNOG.wide.gz
md5:c635d0a46c21b3ea4f5cac132eb71773
109.5 kB Download
arath_At_Col_0_indark_fraction_201504.protcount.wide.gz
md5:904f3a11f4072b2e125e35acc3469435
240.5 kB Download
arath_At_Col_0_indark_fraction_201504_virNOG.wide.gz
md5:08c0b90c1b864cdc33514b420de39b24
136.8 kB Download
arath_At_Col_0_leaf_fraction_2014.protcount.wide.gz
md5:dd068bff35792b4469c504e6661b5948
178.7 kB Download
arath_At_Col_0_leaf_fraction_2014_virNOG.wide.gz
md5:1ed736ce73f052654743ed8122bd494e
106.0 kB Download
arath_At_Col_0_leaf_fraction_2015.protcount.wide.gz
md5:1d5a046a058a29760543e3ba0b72a1a0
180.0 kB Download
arath_At_Col_0_leaf_fraction_2015_virNOG.wide.gz
md5:68ba2c6f5405eec1225b92ee1cc8b6d7
105.0 kB Download
arath_OP_Arabidopsis_mutantseed_20170323.protcount.wide.gz
md5:e519f8666ec34e64d1e28fb42243ef17
345.6 kB Download
arath_OP_Arabidopsis_mutantseed_20170323_virNOG.wide.gz
md5:5e1ea5d219fefb6c11e134f35ff1e34d
179.3 kB Download
arath_OP_Arabidopsis_sproutsSEC_02102017.protcount.wide.gz
md5:45db863bbe618e389b36a31509b1ff26
323.5 kB Download
arath_OP_Arabidopsis_sproutsSEC_02102017_virNOG.wide.gz
md5:a6e3e61e39d1da43254eb04d0f07b04c
157.3 kB Download
arath_specconcat_protcount.wide.gz
md5:4cdfdac00b7da77c1ce74bcd9409c32c
1.2 MB Download
braol_BroccoliNE_WWC.protcount.wide.gz
md5:50bfc1519f575aef5380a0b6d8ff3a40
354.3 kB Download
braol_BroccoliNE_WWC_virNOG.wide.gz
md5:03eef2e2e8120c6ec6eafa54c472b277
166.9 kB Download
braol_Broccolinuclei_6-2016.protcount.wide.gz
md5:72d0648b2290d4fa32fbe6d2c1a1c297
252.5 kB Download
braol_Broccolinuclei_6-2016_virNOG.wide.gz
md5:bd131fbc149a9b793492e52805f8a603
123.3 kB Download
braol_Broccolinuclei_IEF_9-2016.protcount.wide.gz
md5:a122eaf0a591bf32e269cfa4786746ca
211.3 kB Download
braol_Broccolinuclei_IEF_9-2016_virNOG.wide.gz
md5:1c82ca96eefde6e2ef771083f37e2b8c
92.6 kB Download
braol_OP_Broccoli_leaf_IEX2_20170317.protcount.wide.gz
md5:6eeda08c4ea475d31a758c32aa7cfbb3
340.8 kB Download
braol_OP_Broccoli_leaf_IEX2_20170317_virNOG.wide.gz
md5:8bfadffec62e57cf5f69252f2cee4e28
166.8 kB Download
braol_specconcat_protcount.wide.gz
md5:a11769210e5eb94507e1982cc939d16c
930.5 kB Download
cansa_OP_Hemp_seed_IEX_20170724.protcount.wide.gz
md5:b31fcb3b167a702393699ff4a8a1cdc0
196.2 kB Download
cansa_OP_Hemp_seed_IEX_20170724_virNOG.wide.gz
md5:b782d252025e24b86fac404f57b839c5
150.1 kB Download
cerri_Fern_Frond_WWC_20151217.protcount.wide.gz
md5:9f6b4b8c7232689a4cc2c5775144eb89
616.4 kB Download
cerri_Fern_Frond_WWC_20151217_virNOG.wide.gz
md5:0539bfa2a23d587e14a79f23a931be28
131.9 kB Download
cerri_OP_Fernfrond_SEC_112016.protcount.wide.gz
md5:90a458ebfa947df0e43d6a9975d1c3fe
628.7 kB Download
cerri_OP_Fernfrond_SEC_112016_virNOG.wide.gz
md5:fcd8b9386a6750820ed65f491a17616e
108.1 kB Download
cerri_specconcat_protcount.wide.gz
md5:bf4131e4002a6699afbe1597e9a105d6
1.1 MB Download
chlre_Chlamydomonas_WWC_9-2016.protcount.wide.gz
md5:ee57bc353cb7f48b9c293e0f1bda08bf
275.4 kB Download
chlre_Chlamydomonas_WWC_9-2016_virNOG.wide.gz
md5:5c0acfddcde29a81a6d8a26c511c758b
213.7 kB Download
chlre_OP_Chlamy_Nuclei_SEC_20170428.protcount.wide.gz
md5:001765810ebb31597c28887cc5f4d363
160.3 kB Download
chlre_OP_Chlamy_Nuclei_SEC_20170428_virNOG.wide.gz
md5:606cdb59a09136e8ddc44502784a874a
124.4 kB Download
chlre_OP_Chlamydomonas_SEC.protcount.wide.gz
md5:18da8311b54ec89ec2869e16a8cff195
266.1 kB Download
chlre_OP_Chlamydomonas_SEC_virNOG.wide.gz
md5:bc69aec6ec2a956fafdb6913f62aec48
201.1 kB Download
chlre_specconcat_protcount.wide.gz
md5:8d0f2708590eee95c83c43c0279fa8b1
531.6 kB Download
chqui_OP_Quinoa_IEX_20170513.protcount.wide.gz
md5:18321baacb083c3c6f8a3dce05e87802
248.3 kB Download
chqui_OP_Quinoa_IEX_20170513_virNOG.wide.gz
md5:364d60d4784d15d59bcdd2fed3c2448a
124.5 kB Download
cocnu_Cocos_nuclei_SEC.protcount.wide.gz
md5:110eed97fa166c15c006df632fe83836
369.1 kB Download
cocnu_Cocos_nuclei_SEC_virNOG.wide.gz
md5:3dd3dc46993a47086576506bda09a7a9
209.5 kB Download
Experiment_Order.csv
md5:6ba9b69833c2d9319c6dfb997e41dd74
2.0 kB Download
Fraction_Details.csv
md5:8cc7067b21a31f73ab9158f2dc9acb55
97.7 kB Download
maize_OP_Corn_20181009_virNOG.wide.gz
md5:c35e3ccb29cce24d70b2483b81932825
191.5 kB Download
orthogroup_annotations.csv.gz
md5:83bed6cee499e8761535bec451b26fde
6.5 MB Download
orysj_Rice_201505.protcount.wide.gz
md5:1aff409e79ea6b2dca7923c228121c18
163.9 kB Download
orysj_Rice_201505_virNOG.wide.gz
md5:11bae97f0a84c80f0f60a96dff28906f
107.5 kB Download
orysj_RiceLeaf_IEX_05192015.protcount.wide.gz
md5:06d818e9722958c02f5719a1fd4268a3
171.1 kB Download
orysj_RiceLeaf_IEX_05192015_virNOG.wide.gz
md5:9e859cc5c6311f4f6dff9e8552b8aec9
111.5 kB Download
orysj_RiceLeaf_SEC_04292016.protcount.wide.gz
md5:7aa41f7660b0dcd706bfb7491342b1f0
411.7 kB Download
orysj_RiceLeaf_SEC_04292016_virNOG.wide.gz
md5:b27f452a77f5d34d17458fa504327391
232.1 kB Download
orysj_specconcat_protcount.wide.gz
md5:ed8ef40625929b4ce7c0d4d653c5532e
637.6 kB Download
panplant_tidy_elution_protcount.csv.gz
md5:d23ee6b665f50db26c250a8f1b039239
25.6 MB Download
panplant_tidy_elution_virNOG.csv.gz
md5:116e0481115136fa5500b010049fe429
31.9 MB Download
panplant_wide_elution_expnorm.csv.gz
md5:1ae6eeed7cab616e22a267940946292c
5.2 MB Download
panplant_wide_elution_expnorm_annot.csv.gz
md5:fc98388322bcac468fdf952e5c206c0a
11.7 MB Download
panplant_wide_elution_virNOG.csv.gz
md5:df05e2cf4882bc056aba5bb88c0b866b
3.3 MB Download
panplant_wide_elution_virNOG_annot.csv.gz
md5:40d2d14c710214aeb9e2b4c9cefe7b52
10.0 MB Download
plant_virNOG_orthology.csv.gz
md5:7070f8cd6e3e3ecfcca3de139b22c2de
5.0 MB Download
selml_OP_SelaginellaSEC_20160309.protcount.wide.gz
md5:526d938312a70dd6ea71a902b041231b
307.5 kB Download
selml_OP_SelaginellaSEC_20160309_virNOG.wide.gz
md5:65b325ed10911477912fbcf4538050eb
151.7 kB Download
selml_selaginella_WWC.protcount.wide.gz
md5:f9975ef7261ecfa1b38f1ceaae30f2d4
180.9 kB Download
selml_selaginella_WWC_virNOG.wide.gz
md5:1ada1350cde2deb0a757757f035e50a3
99.3 kB Download
selml_specconcat_protcount.wide.gz
md5:9ab42822d3b0a7daaca657ebef6febc4
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sollc_OP_Tomato_leaf_IEX2_201270607.protcount.wide.gz
md5:ba573443d61cac61996afc9adc3665ec
168.0 kB Download
sollc_OP_Tomato_leaf_IEX2_201270607_virNOG.wide.gz
md5:1db75c74aa300e99418417144135ea3a
110.3 kB Download
soybn_OP_Soy_sprout_SEC_20172110_virNOG.wide.gz
md5:b387e3b5bf591c73d82c76010f3e5c64
211.6 kB Download
soybn_Soy_SECwithStandards.protcount.wide.gz
md5:2518cf2fb6c9422305c9db2ce60e7827
765.2 kB Download
soybn_Soy_SECwithStandards_virNOG.wide.gz
md5:726ac22b0b9c3b4182d679eeacb5b709
252.4 kB Download
soybn_specconcat_protcount.wide.gz
md5:d493d410cf5de997dae0a6ddfba8962e
710.1 kB Download
wheat_OP_WheatGrassSEC_20170202.protcount.wide.gz
md5:ef8e3ac610d49c46c9a041fc1c3eb210
653.0 kB Download
wheat_OP_WheatGrassSEC_20170202_virNOG.wide.gz
md5:1900d2f6298c7d828aac4212a9eae778
174.4 kB Download
wheat_specconcat_protcount.wide.gz
md5:dbca58672d330af277374b18917a405b
1.8 MB Download
wheat_wgIEF.protcount.wide.gz
md5:730d605d99bf7eab27337b323d6756f8
320.7 kB Download
wheat_wgIEF_virNOG.wide.gz
md5:af52f8813fb6277d50479ab2764e9e9a
88.0 kB Download
wheat_wgSEC1.protcount.wide.gz
md5:28c035af344291d4bb809c05c1b0ae65
521.3 kB Download
wheat_wgSEC1_virNOG.wide.gz
md5:61fec921cfea2b9a6fa468fbbaaa873f
165.4 kB Download
wheat_wheatgermIEX.protcount.wide.gz
md5:4de245e7c17083c54d550b21da11f761
310.5 kB Download
wheat_wheatgermIEX_virNOG.wide.gz
md5:af881134b83036616866091640a81026
92.6 kB Download
wheat_WheatGermSEC_07-2015.protcount.wide.gz
md5:2ae5be9a5f7e0596fd4fad6ecd351483
338.7 kB Download
wheat_WheatGermSEC_07-2015_virNOG.wide.gz
md5:2b2d506497bc079606aab869362db2ad
105.9 kB Download
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