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Computational-MS-DataAnalysis.md 2.84 KiB

2.8 Computational MS data analysis

For peptide and protein identification the acquired MS spectra were analyzed using the MaxQuant version 1.3.0.5 (MPI for Biochemistry, Planegg, Germany) with default parameters (Cox and Mann, 2008). Quantification was performed using the unlabeled quantification option of MaxQuant. The identified spectra were matched against the Ricinus proteome using the peptide search engine Andromeda (Cox et al., 2011). Only proteins containing at least two unique peptides and a minimum of three valid values in at least one group were quantified. A full list of all identified peptides from the proteome experiment is presented in Supplemental Table S1. All identified Ricinus proteins were analyzed by bidirectional BLAST against the Arabidopsis proteome (Altschul et al., 1990). Organelle distribution within the collected fractions was assayed using a set of marker proteins. Proteins were assigned as organelle markers if the experimental localization of their Arabidopsis homologues in the SUBA 5.0 database (Hooper et al., 2017; Hooper et al., 2022) corresponded with their sequence-based localization prediction in Ricinus. We predicted protein localization to peroxisomes, mitochondria, and plastids manually and using the publicly available tools PPero, PredPlantPTS1, and TargetP (Emanuelsson et al., 2000; Reumann et al., 2012; Wang et al., 2015).

  • Cox, J., and Mann, M. (2008). MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372. doi: 10.1038/nbt.1511
  • Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., and Mann, M. (2011). Andromeda: A peptide search engine integrated into the maxQuant environment. J. Proteome Res. 10, 1794–1805. doi: 10.1021/pr101065j
  • Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410. doi: 10.1016/S0022-2836(05) 80360-2
  • Hooper, C. M., Castleden, I. R., Tanz, S. K., Aryamanseh, N., and Millar, A. H. (2017). SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations. Nucleic Acids Res. 45, D1064–D1074. doi: 10.1093/nar/gkw1041
  • Hooper, C. M., Castleden, I., Tanz, S. K., Grasso, S. V., Aryamanesh, N., and Millar, A. H. (2022). Subcellular Localisation database for Arabidopsis proteins version 5 (The University of Western Australia). doi: 10.26182/8dht-4017
  • Emanuelsson, O., Nielsen, H., Brunak, S., and von Heijne, G. (2000). Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300, 1005–1016. doi: 10.1006/jmbi.2000.3903
  • Reumann, S., Buchwald, D., and Lingner, T. (2012). PredPlantPTS1: A web server for the prediction of plant peroxisomal proteins. Front. Plant Sci. 3. doi: 10.3389/ fpls.2012.00194