Computational protocol: Proteomics analysis reveals differentially activated pathways that operate in peanut gynophores at different developmental stages

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Protocol publication

[…] Raw data files obtained from the Orbitrap were converted into MGF files using Proteome Discoverer 1.2 (Thermo, USA). Protein annotation was performed using the Mascot search engine (Matrix Science, UK; version 2.3.02) against the peanut transcriptome database, which contained 72, 527 unigenes []. The parameters for protein identification are listed in Additional file : Table S9, and the false discovery rate (FDR) was set to 0.05 for both peptides and proteins.Functional annotation of the proteins was performed using the Blast2 GO program against the non-redundant protein database at NCBI []. KEGG pathway analysis was performed by comparing the identified proteins with the KEGG database (http://www.genome.jp/kegg/). COG classification was carried out by comparing the identified proteins with the Cluster of Orthologous Groups database (http://www.ncbi.nlm.nih.gov/COG/). […]

Pipeline specifications

Software tools Proteome Discoverer, Mascot Server
Databases KEGG KEGG PATHWAY
Application MS-based untargeted proteomics
Diseases Multiple Sclerosis
Chemicals Nitrogen