Mass spectrometry proteomic diagnosis: enacting the validation paradigm

In this review, we present an overview of the main aspects related to the statistical evaluation of medical tests for diagnosis and prognosis. Measures of diagnostic performance for binary tests, such as sensitivity, specificity, and predictive values, are introduced, and extensions to the case of continuous-outcome tests are detailed. Special focus is placed on the receiver operating characteristic (ROC) curve and its estimation, with the topic of covariate adjustment receiv...

Motivation: Proteomic mass spectrometry analysis is becoming routine in clinical diagnostics, for example to monitor cancer biomarkers using blood samples. However, differential proteomics and identification of peaks relevant for class separation remains challenging. Results: Here, we introduce a simple yet effective approach for identifying differentially expressed proteins using binary discriminant analysis. This approach works by data-adaptive thresholding of protein exp...

Metabolomic data can potentially enable accurate, non-invasive and low-cost prediction of coronary artery disease. Regression-based analytical approaches however might fail to fully account for interactions between metabolites, rely on a priori selected input features and thus might suffer from poorer accuracy. Supervised machine learning methods can potentially be used in order to fully exploit the dimensionality and richness of the data. In this paper, we systematically imp...

Machine Science, or Data-driven Research, is a new and interesting scientific methodology that uses advanced computational techniques to identify, retrieve, classify and analyse data in order to generate hypotheses and develop models. In this paper we describe three recent biomedical Machine Science studies, and use these to assess the current state of the art with specific emphasis on data mining, data assessment, costs, limitations, skills and tool support.

The developing field of enhanced diagnostic techniques in the diagnosis of infectious diseases, constitutes a crucial domain in modern healthcare. By utilizing Gas Chromatography-Ion Mobility Spectrometry (GC-IMS) data and incorporating machine learning algorithms into one platform, our research aims to tackle the ongoing issue of precise infection identification. Inspired by these difficulties, our goals consist of creating a strong data analytics process, enhancing machine ...

With the recent developments in proteomic technologies, a complete human proteome project (HPP) appears feasible for the first time. However, there is still debate as to how it should be designed and what it should encompass. In "proteomics speak", the debate revolves around the central question as to whether a gene-centric or a protein-centric proteomics approach is the most appropriate way forward. In this paper, we try to shed light on what these definitions mean, how larg...

As the volume and complexity of data continue to expand across various scientific disciplines, the need for robust methods to account for the multiplicity of comparisons has grown widespread. A popular measure of type 1 error rate in multiple testing literature is the false discovery rate (FDR). The FDR provides a powerful and practical approach to large-scale multiple testing and has been successfully used in a wide range of applications. The concept of FDR has gained wide a...

Research on decision support applications in healthcare, such as those related to diagnosis, prediction, treatment planning, etc., have seen enormously increased interest recently. This development is thanks to the increase in data availability as well as advances in artificial intelligence and machine learning research. Highly promising research examples are published daily. However, at the same time, there are some unrealistic expectations with regards to the requirements f...

Many pressing medical challenges - such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers - have long been hindered by limitations in our ability to quantify proteins in single cells. Mass-spectrometry (MS) is poised to transcend these limitations by developing powerful methods to routinely quantify thousands of proteins and proteoforms across many thousands of single cells. We outline specific technological developments and ideas th...

The integration of bioinformatics predictions and experimental validation plays a pivotal role in advancing biological research, from understanding molecular mechanisms to developing therapeutic strategies. Bioinformatics tools and methods offer powerful means for predicting gene functions, protein interactions, and regulatory networks, but these predictions must be validated through experimental approaches to ensure their biological relevance. This review explores the variou...