Data processing and protein identification were performed using Spectrum Mill (Ver. B.06.00.201, Agilent Technologies, USA) against an organism-specific database (NCBI taxa: Malvales; as of October 2016). Carbamidomethylation was selected as the fixed modification parameter and trypsin as the digestion enzyme with the maximum number of missed cleavages equal to 2. The MS searches were auto-validated at a false discovery rate (FDR) of 1.2%, followed by the generation of protein–protein comparison files and data export to Mass Profiler Professional (MPP v 14.9.1, Agilent Technologies, USA) for further analysis. The data files were then processed by principle component analysis (PCA) using the MPP software.
Mass profiler professional mpp v 14
Manufactured by Agilent Technologies
Sourced in United States
Mass Profiler Professional (MPP v 14.9.1) is a software tool designed for multivariate data analysis of mass spectrometry-based omics data. It provides statistical and pattern recognition methods to identify and compare significant changes in metabolites, proteins, or other molecules across experimental conditions.
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Lab products found in correlation
2 protocols using mass profiler professional mpp v 14
1
Proteomic Analysis of Malvales Plants
2
Proteomic Analysis of Killdeer Species
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A Swiss-Prot database search for protein and peptide identification matched with Charadrius vociferus species was performed using the Spectrum Mill MS Proteomics Workbench (Agilent Technologies, Santa Clara, CA, USA). Carbamidomethylation was selected as the fixed modification parameter and trypsin as the digestive enzyme, with the maximum number of cleavage equal to 2. Auto-validation was set for MS searches at a false discovery rate (FDR) of 1.2% and data export to Mass Profiler Professional (MPP v 14.9.1, Agilent Technologies, Santa Clara, CA, USA) for further analysis. The software confirmed the identified protein and the post-translation modifications if present, and the data files were then processed by principal component analysis (PCA) using the MPP software.
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