DOI: 10.6084/m9.figshare.12251273
title: Plasma membrane proteomics

description: The resulting MS/MS data were processed using Maxquant search engine (v.1.5.2.8). Spectra search was performed against the Soybean genome sequence databases downloaded from the phytozome database (https://phytozome.jgi.doe.gov/pz/portal.html, containing 88,647 unigenes) concatenated with reverse decoy database. FDR of protein identification and PSM identification was set to 1%. To be considered diferentially expressed, proteins were required to exhibit a P value ≤ 0.05 calculated by the software. For protein abundance ratios measured using TMT, we considered a 1.3-fold change and a P value &lt; 0.05 as the thresholds for identifying significant changes. Gene Ontology (GO) annotation proteome was derived from the UniProt-GOA database (www. http://www.ebi.ac.uk/GOA/). Firstly, Converting identified protein ID to UniProt ID and then mapping to GO IDs by protein ID. If some identified proteins were not annotated by UniProt-GOA database, the InterProScan soft would be used to annotated protein’s GO functional based on protein sequence alignment method. Then proteins were classified by Gene Ontology annotationbased on three categories: biological process, cellular component and molecular function. Identified proteins domain functional description were annotated by InterProScan (a sequence analysis application) based on protein sequence alignment method, and the InterPro domain database was used. InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Kyoto Encyclopedia of Genes and Genomes (KEGG)database was used to annotate protein pathway. Firstly, using KEGG online service tools KAAS to annotated protein’s KEGG database description. Then mapping the annotation result on the KEGG pathway database using KEGG online service tools KEGG mapper. We used wolfpsort a subcellular localization predication soft to predict subcellular localization. Wolfpsort an updated version of PSORT/PSORT II for the prediction of eukaryotic sequences. Proteins were classified by GO annotation into three categories: biological process, cellular compartment and molecular function. For each category, a two-tailed Fisher’s exact test was employed to test the enrichment of the differentially expressed protein against all identified proteins. The GO with a corrected p-value &lt; 0.05 is considered significant. Encyclopedia of Genes and Genomes (KEGG) database was used to identify enriched pathways by a two-tailed Fisher’s exact test to test the enrichment of the differentially expressed protein against all identified proteins. The pathway with a corrected p-value &lt; 0.05 was considered significant. These pathways were classified into hierarchical categories according to the KEGG website. For each category proteins, InterPro (a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites) database was researched and a two-tailed Fisher’s exact test was employed to test the enrichment of the differentially expressed protein against all identified proteins. Protein domains with a p-value &lt; 0.05 were considered significant. For further hierarchical clustering based on different protein functional classification (such as: GO, Domain, Pathway, Complex). We first collated all the categories obtained after enrichment along with their P values, and then filtered for those categories which were at least enriched in one of the clusters with P value &lt;0.05. This filtered P value matrix was transformed by the function x = −log10 (P value). Finally these x values were z-transformed for each functional category. These z scores were then clustered by one-way hierarchical clustering (Euclidean distance, average linkage clustering) in Genesis. Cluster membership were visualized by a heat map using the “heatmap.2” function from the “gplots” R-package.