LC-QTOF-MS Analysis Raw Data for the Phytochemical Profiling of the SF-AR Herb Pair

In this study, the phytochemical profile of the TCM herb pair Sophorae Flavescentis Radix–Astragali Radix (SF-AR) was systematically characterized. The characterization was performed using a high-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) system. This dataset contains the analysis of the SF-AR herb pair extract, alongside analysis of the individual SF and AR extracts, which were used to determine the botanical origin of the characterized constituents.Raw data was acquired in both positive and negative electrospray ionization modes using an Agilent 1260 Infinity HPLC System coupled with a Sciex TripleTOF 5600+ Quadrupole Time-of-Flight tandem mass spectrometer. The acquisition method combined TOF MS full scan and data-dependent CID fragmentation scans (IDA mode). Data processing and constituent identification were performed using Sciex PeakView® and MasterView™ software. The analytical strategy integrated in-house database matching, structural relevance filtering, and untargeted compound screening.This dataset provides a comprehensive chemical basis for the phytochemical profiling of the SF-AR herb pair, which is critical for linking its anti-hepatocellular carcinoma efficacy to its bioactive constituents. This repository stores the raw mass spectrometry data (.wiff and .wiffscan files) for the six analysis performed: SF-AR herb pair (positive and negative ion modes), SF alone (positive and negative ion modes), and AR alone (positive and negative ion modes). This resource is intended for the research community to validate the constituents identified in this study and to support further exploration of the herb pair's complex chemical composition.