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+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02402.raw filter=lfs diff=lfs merge=lfs -text
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+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02412.raw filter=lfs diff=lfs merge=lfs -text
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+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02408.raw filter=lfs diff=lfs merge=lfs -text
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+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02421.raw filter=lfs diff=lfs merge=lfs -text
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+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02336.raw filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -381,6 +381,3 @@ Icon
 Network Trash Folder
 Temporary Items
 .apdisk
-
-
-*.raw
\ No newline at end of file

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README.md

-# ricinus_proteome_arc
+# Wrobel-2023-CastorBeanEndospermProteome
 
-Legacy data on Ricinus proteome from Nicole Linka and Thomas Wrobel 
+## Publication
 
-## setting up this arc
+Wrobel TJ, Brilhaus D, Stefanski A, Stühler K, Weber APM, Linka N. Mapping the castor bean endosperm proteome revealed a metabolic interaction between plastid, mitochondria, and peroxisomes to optimize seedling growth. Front Plant Sci. 2023 Oct 6;14:1182105. doi: 10.3389/fpls.2023.1182105. PMID: 37868318; PMCID: PMC10588648.
 
-> using arcCommander v0.3.1
+## License
 
-```bash
-arc init
-arc i create -i "Ricinus proteome"
-mkdir _NicolesData; touch _NicolesData/.gitkeep
-```
+Copyright © 2023 Wrobel, Brilhaus, Stefanski, Stühler, Weber and Linka
 
-## add raw dataset as retrieved from Anja Stefanski via Sciebo (06.04.2022)
+This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
 
-### setup assay structure
+## Data availability
 
-```bash
-arc assay add -s "2012_ricinus_proteome_wrobel" -a "2012_proteome_data_bmfz_stefanski"
-```
-
-### run md5s on downloaded data
-
-```bash
-md5 ~/Downloads/Daten\ Linka/*.raw > _NicolesData/raw_data_md5s.txt
-```
-
-### Add large data to gitignore for now...
-
-```bash
-printf "\n*.raw" >> .gitignore
-```
-
-### add downloaded data to arc
-
-```bash
-mv ~/Downloads/Daten\ Linka/Messliste_Wrobel.xlsx _NicolesData/
-mv ~/Downloads/Daten\ Linka/*.raw assays/2012_proteome_data_bmfz_stefanski/dataset
-```
-
-### sync arc with GitLab
-
-```bash
-arc sync -m "add raw data from bmfz"
-```
+The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD040932.
\ No newline at end of file

_NicolesData/README.md

-# meeting notes
-
-## 11.04.2022
-
-### orig idea
-
-- new transporter in peroxisome membrane
-- proteome sequence all organelle fractions
-  - confirm peroxisomal location
-
-### special issue
-
-- cooperation multiple organelles in cell
-- degradation of ricinus storage amongst organelles (- cytosol missing)
-- Special issue “Photosynthetic and photorespiratory organelles: metabolism, dynamics, and signaling” Frontiers of Plant Science
-
-### sfb 
-
-- associate fractions with marker proteins (based on publications)
-- project workflow
-
-
-### TODO: upload data to PRIDE
-
-- swate template
-- 
\ No newline at end of file

_NicolesData/raw_data_md5s.txt

-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02336.raw) = df329fb56d693c51d3f4f9e9d47bf3f6
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02337.raw) = 20f1c046899975cb9bba5fec47aed31d
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02339.raw) = 8ec359bfc6bd2f2edfd28ea21f28bd2a
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02340.raw) = a36bf4b606dc008b873cb6fa22582027
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02342.raw) = f09d2eb6867a304f4dec8e5465ea96f2
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02343.raw) = 14da4e792980dea5cf8e75f39d8c58ad
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02345.raw) = df4a4da1c7d9917d50062c73f13054d3
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02346.raw) = 9d1e5fbbe9db3422d74c9403ce9472da
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02396.raw) = 9cece1c71528c47f3fa13b05bedb95fb
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02397.raw) = 5dcd5bd48c3ffc0facc61171e1a43919
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02399.raw) = b6b2d9c4cf72affefaede1c17e3dbd2c
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02400.raw) = 7369ddf770d2e17d12f098fd7df656ef
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02402.raw) = 08d7429cebe720c73d8f6a3dd3570933
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02403.raw) = ffb4fd4313959d6ce387d2cc099fc00f
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02405.raw) = aad6229645856756a1226c691b98fc83
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02406.raw) = 32895aa1155cda14463f52bf9c575740
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02408.raw) = 39f9bde1f8fd35de6f0886a479f85286
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02409.raw) = 124d15829581e8b193f1949e3f14fc63
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02412.raw) = fa0bb5abb901d306bad4d985251537af
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02413.raw) = eef196922615cd0311c65b088b6cf65e
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02415.raw) = fc61cf631605902e7b5fb014520bf8c9
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02416.raw) = c42adb8280c8d2fcfef6b593da758cf8
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02418.raw) = 53abf117bfee8c93bfe44621c7e94254
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02419.raw) = 82e68d8c0952bef1404ce4f489cfcac4
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02421.raw) = 23404ff8e4d443a344b00b0639d567f4
-MD5 (/Users/dominikbrilhaus/Downloads/Daten Linka/OE02422.raw) = 1b971dd0963daa184e34d0725c3f59c0

_publication/README.md

+# Publication
+
+downloaded from https://doi.org/10.3389/fpls.2023.1182105
+
+## Citation
+
+Wrobel TJ, Brilhaus D, Stefanski A, Stühler K, Weber APM, Linka N. Mapping the castor bean endosperm proteome revealed a metabolic interaction between plastid, mitochondria, and peroxisomes to optimize seedling growth. Front Plant Sci. 2023 Oct 6;14:1182105. doi: 10.3389/fpls.2023.1182105. PMID: 37868318; PMCID: PMC10588648.
+
+## License
+
+Copyright © 2023 Wrobel, Brilhaus, Stefanski, Stühler, Weber and Linka
+
+This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
+
+## Supplementary material
+
+https://www.frontiersin.org/articles/10.3389/fpls.2023.1182105/full#supplementary-material