Trends and Innovations in Tools for Processing Chromatographic Data Using Mass Spectrometry Detection: A Systematic Review

Chromatographic data processing represents an increasing challenge in analytical science, particularly due to the complexity of samples and the large volume of data generated by chromatographic techniques coupled with mass spectrometry (MS). This paper presents a systematic review of technological innovations over the last six years in the development of computational tools for processing these data. The review follows the PRISMA protocol, with a search conducted across five databases (SciFinder, Scopus, Web of Science, Embase, and ScienceDirect), utilizing strategies based on indexed descriptors and Boolean combinations. Thirty-three studies were selected that met the criteria of originality, applicability, and innovation in analytical tools. The results reveal significant advancements in algorithms for peak detection, alignment, and deconvolution, with an emphasis on machine learning, deep learning, and multivariate resolution approaches. Tools such as DeepResolution, SeA-M2Net, SLAW, QPMASS, autoGCMSDataAnal, and AntDAS demonstrate automation, scalability, and higher accuracy in critical tasks such as noise filtering, baseline correction, and compound identification. The analysis also highlights the progress of open-source software, which promotes greater access and interoperability. Although challenges such as the need for annotated data and standardization remain, recent advancements signal a shift toward more robust, accessible, and adaptable solutions for chromatographic data processing, expanding the potential of analyses across various scientific and industrial contexts. In this review, 'peak deconvolution' refers to separating co-eluting chromatographic signals, while 'spectral deconvolution' denotes reconstructing pure MS/MS spectra from mixed fragments."