.gitattributes

 **/dataset/** filter=lfs diff=lfs merge=lfs -text
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+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02402.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02416.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02403.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02415.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02399.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02400.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02405.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02413.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02412.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02406.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02345.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02422.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02346.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02408.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02409.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02421.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02419.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02343.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02342.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02418.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02340.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02397.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02396.raw filter=lfs diff=lfs merge=lfs -text
+/assays/2012_proteome_data_bmfz_stefanski/dataset/OE02337.raw filter=lfs diff=lfs merge=lfs -text
+/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

LICENSE

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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"
-```
\ No newline at end of file
+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/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

assays/2_2-FAME-analysis/README.md

+
+## FAME-analysis
+
+![fpls-14-1182105-g002.jpg](dataset/fpls-14-1182105-g002.jpg)
+
+**Figure 2**
+
+Storage oil mobilization in castor bean endosperm. (A) Relative fresh weight of the endosperm in dry seeds (-1d), imbibed seeds (0d) and 1- to 7-day old dark-grown castor bean seedlings (1-7d) as percentage of fresh weight of the whole plant. Data represent arithmetic means ± SD of 3 biological replicates. (B) Relative ricinoleic acid content of the endosperm from seeds and seedlings. Samples were normalized to the average fresh weight of on endosperm and expressed as percentages of their initial quantities determined in dry seeds (-1d). Error bars show standard deviations of the means of at least three biological replicates.
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assays/2_2-FAME-analysis/protocols/FAME-analysis.md

+# 2.2 Fatty acid methylester (FAME) analysis
+
+The ricinoleic acid content in the castor bean endosperm was determined using gas chromatography-mass spectrometry (GC- MS)-based fatty acid methyl ester (FAME) method (Hielscher et al., 2017). Endosperm tissue was dissected from dry seeds, 24h- imbibed seeds and 1- to 6-day old dark-grown seedlings by removing the embryo and roots with the blunt end of a scalpel blade, weighed and shock frozen in liquid nitrogen.
+FAME analyses were generated by acid catalyzed methyl-ester formation using methanolic HCl as described by Hielscher et al. (2017). 20 mg endosperm was incubated at 90°C for one hour in 1 ml 3 N methanolic-HCl containing heptadecanoic acid (C17:0) as internal standard. The subsequent extraction of fatty acids from the sample was performed with 1 ml n-hexane and 1 ml 1% (w/v) sodium chloride. Samples were centrifuged at 2,000 g for five minutes. The resulting upper hexane phase was transferred into GC vials. The FAME extracts (1:100 diluted) were analyzed by GC Agilent 7890A gas chromatograph coupled to Waters GCT-TOF Premier mass spectrometer equipped with a Gerstel MPS2XL auto sampler.
+Quantification and identification of the detected fatty acids was carried out with QuantLynx and MassLynx, respectively. Peaks were integrated and the resulting areas used for determination of relative changes in the abundance of the castor oil-specific ricinoleic acid. As the Ricinus endosperm started to gain fresh weight during seedling development due to water uptake, the fatty acid quantities were normalized to the fresh weight of an average endosperm. All samples were analyzed in three biological replicates.
+
+
+- Hielscher, B., Charton, L., Mettler-Altmann, T., and Linka, N. (2017). Analysis of peroxisomal b-oxidation during storage oil mobilization in Arabidopsis thaliana Seedlings. Methods Mol. Biol. 1595, 291–304. doi: 10.1007/978-1-4939-6937-1_27
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assays/2_3-OrganellesFromEndosperm/README.md

+
+
+![fpls-14-1182105-g003.jpg](dataset/fpls-14-1182105-g003.jpg)
+
+**Figure 3** 
+
+Isolation of organelles from etiolated castor bean seedlings. Four fractions of the sucrose density step gradient after centrifugation were taken from the gradient for various analyses at the interface 30% - 44% (w/w) sucrose solution (F1), 44% - 48% (w/w) sucrose solution (F2), 48% - 49% (w/w) sucrose solution (F3), and 50% - 54% (w/w) sucrose solution (F4).
\ No newline at end of file