Nejvíce citovaný článek - PubMed ID 31728648
Human nails have recently become a sample of interest for toxicological purposes. Multiple studies have proven the ability to detect various analytes within the keratin matrix of the nail. The analyte of interest in this study is fentanyl, a highly dangerous and abused drug in recent decades. In this proof-of-concept study, ATR-FTIR was combined with machine learning methods, which are effective in detecting and differentiating fentanyl in samples, to explore whether nail samples are distinguishable from individuals who have used fentanyl and those who have not. PLS-DA and SVM-DA prediction models were created for this study and had an overall accuracy rate of 84.8% and 81.4%, respectively. Notably, when classification was considered at the donor level-i.e., determining whether the donor of the nail sample was using fentanyl-all donors were correctly classified. These results show that ATR-FTIR spectroscopy in combination with machine learning can effectively differentiate donors who have used fentanyl and those who have not and that human nails are a viable sample matrix for toxicology.
- Klíčová slova
- ATR–FTIR, PLS-DA, SVM-DA, fentanyl, fingernails, machine learning, toenails,
- MeSH
- fentanyl * analýza MeSH
- lidé MeSH
- nehty * chemie MeSH
- spektroskopie infračervená s Fourierovou transformací metody MeSH
- strojové učení * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- fentanyl * MeSH
Feature-based molecular networking (FBMN) is a popular analysis approach for liquid chromatography-tandem mass spectrometry-based non-targeted metabolomics data. While processing liquid chromatography-tandem mass spectrometry data through FBMN is fairly streamlined, downstream data handling and statistical interrogation are often a key bottleneck. Especially users new to statistical analysis struggle to effectively handle and analyze complex data matrices. Here we provide a comprehensive guide for the statistical analysis of FBMN results, focusing on the downstream analysis of the FBMN output table. We explain the data structure and principles of data cleanup and normalization, as well as uni- and multivariate statistical analysis of FBMN results. We provide explanations and code in two scripting languages (R and Python) as well as the QIIME2 framework for all protocol steps, from data clean-up to statistical analysis. All code is shared in the form of Jupyter Notebooks ( https://github.com/Functional-Metabolomics-Lab/FBMN-STATS ). Additionally, the protocol is accompanied by a web application with a graphical user interface ( https://fbmn-statsguide.gnps2.org/ ) to lower the barrier of entry for new users and for educational purposes. Finally, we also show users how to integrate their statistical results into the molecular network using the Cytoscape visualization tool. Throughout the protocol, we use a previously published environmental metabolomics dataset for demonstration purposes. Together, the protocol, code and web application provide a complete guide and toolbox for FBMN data integration, cleanup and advanced statistical analysis, enabling new users to uncover molecular insights from their non-targeted metabolomics data. Our protocol is tailored for the seamless analysis of FBMN results from Global Natural Products Social Molecular Networking and can be easily adapted to other mass spectrometry feature detection, annotation and networking tools.
This study reports on the successful use of a machine learning approach using attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy for the classification and prediction of a donor's sex from the fingernails of 63 individuals. A significant advantage of ATR FT-IR is its ability to provide a specific spectral signature for different samples based on their biochemical composition. The infrared spectrum reveals unique vibrational features of a sample based on the different absorption frequencies of the individual functional groups. This technique is fast, simple, non-destructive, and requires only small quantities of measured material with minimal-to-no sample preparation. However, advanced multivariate techniques are needed to elucidate multiplex spectral information and the small differences caused by donor characteristics. We developed an analytical method using ATR FT-IR spectroscopy advanced with machine learning (ML) based on 63 donors' fingernails (37 males, 26 females). The PLS-DA and ANN models were established, and their generalization abilities were compared. Here, the PLS scores from the PLS-DA model were used for an artificial neural network (ANN) to create a classification model. The proposed ANN model showed a greater potential for predictions, and it was validated against an independent dataset, which resulted in 92% correctly classified spectra. The results of the study are quite impressive, with 100% accuracy achieved in correctly classifying donors as either male or female at the donor level. Here, we underscore the potential of ML algorithms to leverage the selectivity of ATR FT-IR spectroscopy and produce predictions along with information about the level of certainty in a scientifically defensible manner. This proof-of-concept study demonstrates the value of ATR FT-IR spectroscopy as a forensic tool to discriminate between male and female donors, which is significant for forensic applications.
- Klíčová slova
- ATR FT-IR spectroscopy, artificial neural network (ANN), female, machine learning, male, partial least-square discriminant analysis (PLS-DA),
- MeSH
- algoritmy * MeSH
- lidé MeSH
- nehty * MeSH
- neuronové sítě MeSH
- odběr biologického vzorku MeSH
- spektroskopie infračervená s Fourierovou transformací metody MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Machine learning has become a powerful tool for systems biologists, from diagnosing cancer to optimizing kinetic models and predicting the state, growth dynamics, or type of a cell. Potential predictions from complex biological data sets obtained by "omics" experiments seem endless, but are often not the main objective of biological research. Often we want to understand the molecular mechanisms of a disease to develop new therapies, or we need to justify a crucial decision that is derived from a prediction. In order to gain such knowledge from data, machine learning models need to be extended. A recent trend to achieve this is to design "interpretable" models. However, the notions around interpretability are sometimes ambiguous, and a universal recipe for building well-interpretable models is missing. With this work, we want to familiarize systems biologists with the concept of model interpretability in machine learning. We consider data sets, data preparation, machine learning methods, and software tools relevant to omics research in systems biology. Finally, we try to answer the question: "What is interpretability?" We introduce views from the interpretable machine learning community and propose a scheme for categorizing studies on omics data. We then apply these tools to review and categorize recent studies where predictive machine learning models have been constructed from non-sequential omics data.
- Klíčová slova
- deep learning, explainable artificial intelligence, interpretable machine learning, metabolomics, multi-omics, proteomics, transcriptomics,
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
