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_publication/README.md

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 downloaded from https://doi.org/10.3389/fpls.2023.1182105
 
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 ## 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.
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 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.
 
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 ## Supplementary material
 
 https://www.frontiersin.org/articles/10.3389/fpls.2023.1182105/full#supplementary-material

assays/2_8-Computational-MS-DataAnalysis/README.md

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+Source: https://www.frontiersin.org/articles/10.3389/fpls.2023.1182105/full#supplementary-material
+
+## Table 1
+
+SUPPLEMENTARY TABLE 1
+List of proteins isolated from endosperm tissue of etiolated castor bean seedlings, which were identified and quantified in the density-gradient fractions containing the total proteins (T1 to T4) and membrane proteins (M1 to M4). Three biological replicates were subjected to proteome analysis. Only proteins contained at least two unique peptides and a minimum of three valid values in at least one fraction (total or membrane) were classified as “identified”. Values represent the absolute abundance of the proteins calculated by the sum of the peptide signal intensities.
+
+## Table 2
+
+SUPPLEMENTARY TABLE 2
+List of castor bean proteins that have been defined as specific to peroxisomes, plastids, mitochondria, cytosol, vacuole, ER, Golgi, and nucleus based on (1) in silico prediction tools for their subcellular localization within the cell and (2) experimental data from GFP and/or MS assays of their corresponding Arabidopsis homologue using SUBA 5.0.
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+
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+SUPPLEMENTARY FIGURE 1
+Classification of the identified castor bean endosperm proteins from a soluble and membrane fraction enriched with peroxisomes (A), mitochondria (B), and plastids (C). The classification is based on UniProt database. Numbers in percent refer to the number of proteins that have been assigned to a certain metabolic pathway relative to the total proteins of all metabolic pathways of the respective organelle.
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assays/2_9-StatisticalAnalysis-ProteomeDeconvolution/README.md

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+Source: https://www.frontiersin.org/articles/10.3389/fpls.2023.1182105/full#supplementary-material
+
+## "Table 3.xlsx"
+
+SUPPLEMENTARY TABLE 3
+Deconvolution-based assignment of the MS-identified proteins from etiolated castor bean seedlings to their subcellular localization. Linear regression (LR), quadratic programming (QP), support vector regression (SVR), and non-negative matrix factorization (NMF) were applied to assign 2258 identified endosperm proteins to a specific cell compartment. The assignment of a subcellular compartment was made when at least three of the four deconvolution approaches resulted in a matching localization (consensus).
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+## "Table 4.xlsx"
+
+SUPPLEMENTARY TABLE 4
+List of proteins found in peroxisomes, mitochondria, and plastids isolated from castor bean etiolated endosperm in this study. For functional annotation of proteins and their assignment to biological processes or metabolic pathways, gene ontology analysis was performed by Uniprot.
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+
+## "Image 1.jpg"
+
+SUPPLEMENTARY FIGURE 1
+Classification of the identified castor bean endosperm proteins from a soluble and membrane fraction enriched with peroxisomes (A), mitochondria (B), and plastids (C). The classification is based on UniProt database. Numbers in percent refer to the number of proteins that have been assigned to a certain metabolic pathway relative to the total proteins of all metabolic pathways of the respective organelle.
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