This dataset contains LC-MS raw files and mass feature-SNP marker association results filtered by -log(p) < 5 Files in the metaboliteFastGlm_boxCoxTransformed sub-directory contain genome-wide association study (GWAS) results from maize secondary metabolites in tab-delimited format. Data were generated from association analyses of ~4,000 mass spectrometry features with ~80M single nucleotide polymorphism (SNP) markers with the generalized linear model implemented in the FastGLM pipeline, and filtered by statistical significance of association (-log(p) > 5). This dataset allows colleagues in the maize genetics and biochemistry field to quickly identify high-resolution genetic loci that are significantly associated with biochemical traits of interests, and generate testable hypothesis to infer the genetic regulation of these traits. In addition, files in the Raw_MS_Files sub-directory contains raw liquid chromatography-mass spectrometry (LC-MS) result files generated by a ThermoQ-Exactive Plus system, organized into further subfolders based on the type of biological tissues and modes of electron spray ionization. The Raw_MSMS_Files sub-directory contains raw LC tandem MS result files generated by the same Thermo Q-Exactive Plus system with the same LC inlet gradient. For more details, see readme.txt.