assays/2_4-EnzymeActivityOrganellarMarkers/README.md

+![fpls-14-1182105-t001.jpg](dataset\fpls-14-1182105-t001.jpg)
+
+**Table 1**
+
+Distribution of marker enzyme activities between the fractions.
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assays/2_6-SDS-PAGE-Immunoblotting/README.md

+![fpls-14-1182105-g004.jpg](dataset\fpls-14-1182105-g004.jpg)
+
+**Figure 4** 
+
+Purification of intracellular membranes from castor bean endosperm. Distribution of organellar membrane proteins within the organellar fractions (F1-F4) obtained after sucrose density gradient centrifugation. (A) SDS-PAGE analysis. Each lane was loaded with enriched membrane proteins from each pellet fraction after organelle disruption and ultracentrifugation (F1/F2: 25 µg, F3/F4: 15 µg). Equal loading of the protein gel within the fractions was monitored by staining with colloidal Coomassie G-250 dye. (B) Immunoblot analysis using antibodies raised against the following organelle membrane proteins: chloroplast TIC40, mitochondrial AOX, ER BIP2, and peroxisomal PEX14 proteins. Expected molecular weight for the corresponding castor bean proteins: 50.1 kDa for RcTIC40 (A3QSJ7), 39-41 kDa for RcAOX1/2 (B9RXE2/B9SO38), 73.3 kDa for RcBIP2 (B9RYP6), and 58.3 kDa for RcPEX14 (B9RB25). The membrane was serially probed with antibodies to the indicated marker proteins. The positions of molecular mass markers (in kDa) are indicated at the left.
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assays/2_8-Computational-MS-DataAnalysis/README.md

+
+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.
+
+
+
+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

+![fpls-14-1182105-g005.jpg](dataset\fpls-14-1182105-g005.jpg)
+
+**Figure 5** 
+
+Principal Component Analysis of the Ricinus proteome of the fractions obtained from the sucrose density centrifugation, representing the total proteins (T1 to T4) and the enriched membrane proteins (M1 to M4). In this PCA plot each point represents the identified proteome of one biological experiment.
+
+![fpls-14-1182105-g006.jpg](dataset\fpls-14-1182105-g006.jpg)
+
+**Figure 6** 
+
+Distribution profile of compartment-specific marker proteins in the density-gradient fractions containing the total proteins (T1 to T4) and membrane proteins (M1 to M4). (A) peroxisomes; (B) plastid; (C) mitochondria; (D) ER; (E) nucleus; (F) Golgi; (G) vacuole; (H) cytosol. Relative LFQ represents the sum of Label Free Quantification (LFQ) values for all proteins belonging to an organelle relative to its maximal value.
+
+## Supplementary material
+
+Source for supplementary material: 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).
+
+## "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.
+
+## "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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