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Abstract This protocol describes a high‐throughput absolute quantification protocol for the aromatic essential amino acid, tryptophan (Trp). This procedure consists of a milligram‐scale alkaline hydrolysis followed by an absolute quantification step using a multiple reaction monitoring tandem mass spectrometric (LC‐MS/MS) detection method. The approach facilitates the analysis of a few hundred samples per week by using a 96‐well plate extraction setup. Importantly, the method uses only ∼4 mg of tissue per sample and uses the common alkaline hydrolysis protocol, followed by water extraction that includes L ‐Trp‐d5 as an internal standard to enable the quantification of the absolute level of the bound Trp with high precision, accuracy, and reproducibility. The protocol described herein has been optimized for seed samples for Arabidopsis thaliana , Glycine max , and Zea mays but could be applied to other plant tissues. © 2023 Wiley Periodicals LLC. Basic Protocol : Analysis of protein‐bound tryptophan from seeds 

Abstract In this procedure, we describe a high‐throughput absolute quantification protocol for the protein‐bound sulfur amino acids, cysteine (Cys) and methionine (Met), from plant seeds. This procedure consists of performic acid oxidation that transforms bound Cys into cysteic acid (CysA) and bound Met into methionine sulfone (MetS) followed by acid hydrolysis. The absolute quantification step is performed by multiple reaction monitoring tandem mass spectrometry (LC‐MS/MS). The approach facilitates the analysis of a few hundred samples per week by using a 96‐well plate extraction setup. Importantly, the method uses only ∼4 mg of tissue per sample and uses the common acid hydrolysis protocol, followed by water extraction that includes DL‐Ser‐d3 and L‐Met‐d3 as internal standards to enable the quantification of the absolute levels of the protein‐bound Cys and Met with high precision, accuracy, and reproducibility. The protocol described herein has been optimized for seed samples from Arabidopsis thaliana , Glycine max , and Zea mays but could be applied to other plant tissues. © 2023 Wiley Periodicals LLC. Basic Protocol : Analysis of protein‐bound cysteine and methionine from seeds 

Abstract Motivation Advanced publicly available sequencing data from large populations have enabled informative genome-wide association studies (GWAS) that associate SNPs with phenotypic traits of interest. Many publicly available tools able to perform GWAS have been developed in response to increased demand. However, these tools lack a comprehensive pipeline that includes both pre-GWAS analysis, such as outlier removal, data transformation and calculation of Best Linear Unbiased Predictions or Best Linear Unbiased Estimates. In addition, post-GWAS analysis, such as haploblock analysis and candidate gene identification, is lacking. Results Here, we present Holistic Analysis with Pre- and Post-Integration (HAPPI) GWAS, an open-source GWAS tool able to perform pre-GWAS, GWAS and post-GWAS analysis in an automated pipeline using the command-line interface. Availability and implementation HAPPI GWAS is written in R for any Unix-like operating systems and is available on GitHub (https://github.com/Angelovici-Lab/HAPPI.GWAS.git). Supplementary information Supplementary data are available at Bioinformatics online.