MIND4OLIGOS: Determining the Monoisotopic Mass of Oligonucleotides Observed in High-Resolution Mass Spectrometry.

Oligonucleotide therapeutics have emerged as an important class of drugs offering targeted therapeutic strategies that complement traditional modalities, such as monoclonal antibodies and small molecules. Their unique ability to precisely modulate gene expression makes them vital for addressing previously undruggable targets. A critical aspect of developing these therapies is characterizing their molecular composition accurately. This includes determining the monoisotopic mass of oligonucleotides, which is essential for identifying impurities, degradants, and modifications that can affect the drug efficacy and safety. Mass spectrometry (MS) plays a pivotal role in this process, yet the accurate interpretation of complex mass spectra remains challenging, especially for large molecules, where the monoisotopic peak is often undetectable. To address this issue, we have adapted the MIND algorithm, originally developed for top-down proteomics, for use with oligonucleotide data. This adaptation allows for the prediction of monoisotopic mass from the more readily detectable, most-abundant peak mass, enhancing the ability to annotate complex spectra of oligonucleotides. Our comprehensive validation of this modified algorithm on both in silico and real-world oligonucleotide data sets has demonstrated its effectiveness and reliability. To facilitate wider adoption of this advanced analytical technique, we have encapsulated the enhanced MIND algorithm in a user-friendly Shiny application. This online platform simplifies the process of annotating complex oligonucleotide spectra, making advanced mass spectrometry analysis accessible to researchers and drug developers. The application is available at https://valkenborg-lab.shinyapps.io/mind4oligos/.

A compositional data model to predict the isotope distribution for average peptides using a compositional spline model.

We propose an updated approach for approximating the isotope distribution of average peptides given their monoisotopic mass. Our methodology involves in-silico cleavage of the entire UNIPROT database of human-reviewed proteins using Trypsin, generating a theoretical peptide dataset. The isotope distribution is computed using BRAIN. We apply a compositional data modelling strategy that utilizes an additive log-ratio transformation for the isotope probabilities followed by a penalized spline regression. Furthermore, due to the impact of the number of sulphur atoms on the course of the isotope distribution, we develop separate models for peptides containing zero up to five sulphur atoms. Additionally, we propose three methods to estimate the number of sulphur atoms based on an observed isotope distribution. The performance of the spline models and the sulphur prediction approaches is evaluated using a mean squared error and a modified Pearson's χ2 goodness-of-fit measure on an experimental UPS2 data set. Our analysis reveals that the variability in spectral accuracy, that is, the variability between MS1 scans, contributes more to the errors than the approximation of the theoretical isotope distribution by our proposed average peptide model. Moreover, we find that the accuracy of predicting the number of sulphur atoms based on the observed isotope distribution is limited by measurement accuracy.

R Shiny App for the Automated Deconvolution of NMR Spectra to Quantify the Solid-State Forms of Pharmaceutical Mixtures.

Bioavailability and chemical stability are important characteristics of drug products that are strongly affected by the solid-state structure of the active pharmaceutical ingredient (API). In pharmaceutical development and quality control activities, solid-state NMR (ssNMR) has proved to be an excellent tool for the detection and accurate quantification of undesired solid-state forms. To obtain correct quantitative outcomes, the resulting spectrum of an analytical sample should be deconvoluted into the individual spectra of the pure components. However, the ssNMR deconvolution is particularly challenging due to the following: the relatively large line widths that may lead to severe peak overlap, multiple spinning sidebands as a result of applying Magic Angle Spinning (MAS), and highly irregular peak shapes commonly observed in mixture spectra. To address these challenges, we created a tailored and automated deconvolution approach of ssNMR mixture spectra that involves a linear combination modelling (LCM) of previously acquired reference spectra of pure solid-state components. For optimal model performance, the template and mixture spectra should be acquired under the same conditions and experimental settings. In addition to the parameters controlling the contributions of the components in the mixture, the proposed model includes terms for spectral processing such as phase correction and horizontal shifting that are all jointly estimated via a non-linear, constrained optimisation algorithm. Finally, our novel procedure has been implemented in a fully functional and user-friendly R Shiny webtool (hence no local R installation required) that offers interactive data visualisations, manual adjustments to the automated deconvolution results, and the traceability and reproducibility of analyses.

Is There a Correlation between Multiparametric Assessment in Ultrasound and Intrinsic Subtype of Breast Cancer?

Molecular profile of breast cancer provides information about its biological activity, prognosis and treatment strategies. The purpose of our study was to investigate the correlation between ultrasound features and molecular subtypes of breast cancer. From June 2019 to December 2019, 86 patients (median age 57 years; range 32-88) with 102 breast cancer tumors were included in the study. The molecular subtypes were classified into five types: luminal A (LA), luminal B without HER2 overexpression (LB HER2-), luminal B with HER2 overexpression (LB HER2+), human epidermal growth factor receptor 2 positive (HER2+) and triple negative breast cancer (TNBC). Histopathological verification was obtained in core biopsy or/and post-surgery specimens in all cases. Univariate logistic regression analysis was performed to assess the association between the subtypes and ultrasound imaging features. Experienced radiologists assessed lesions according to the BIRADS-US lexicon. The ultrasound scans were performed with a Supersonic Aixplorer and Supersonix. Based on histopathological verification, the rates of LA, LB HER2-, LB HER2+, HER2+, and TNBC were 33, 17, 17, 16, 19, respectively. Both LB HER2+ and HER2+ subtypes presented higher incidence of calcification (OR = 3.125, p = 0.02, CI 0.0917-5.87) and HER2+ subtype presented a higher incidence of posterior enhancement (OR = 5.75, p = 0.03, CI 1.2257-32.8005), compared to other subtypes. The calcifications were less common in TNBC (OR = 0.176, p = 0.0041, CI 0.0469-0.5335) compared to other subtypes. There were no differences with regard to margin, shape, orientation, elasticity values and vascularity among five molecular subtypes. Our results suggest that there is a correlation between ultrasonographic features assessed according to BIRADS-US lexicon and BC subtypes with HER2 overexpression (both LB HER2+ and HER2+). It may be useful for identification of these aggressive subtypes of breast cancer.

A Compositional Model to Predict the Aggregated Isotope Distribution for Average DNA and RNA Oligonucleotides.

Structural modifications of DNA and RNA molecules play a pivotal role in epigenetic and posttranscriptional regulation. To characterise these modifications, more and more MS and MS/MS- based tools for the analysis of nucleic acids are being developed. To identify an oligonucleotide in a mass spectrum, it is useful to compare the obtained isotope pattern of the molecule of interest to the one that is theoretically expected based on its elemental composition. However, this is not straightforward when the identity of the molecule under investigation is unknown. Here, we present a modelling approach for the prediction of the aggregated isotope distribution of an average DNA or RNA molecule when a particular (monoisotopic) mass is available. For this purpose, a theoretical database of all possible DNA/RNA oligonucleotides up to a mass of 25 kDa is created, and the aggregated isotope distribution for the entire database of oligonucleotides is generated using the BRAIN algorithm. Since this isotope information is compositional in nature, the modelling method is based on the additive log-ratio analysis of Aitchison. As a result, a univariate weighted polynomial regression model of order 10 is fitted to predict the first 20 isotope peaks for DNA and RNA molecules. The performance of the prediction model is assessed by using a mean squared error approach and a modified Pearson's χ2 goodness-of-fit measure on experimental data. Our analysis has indicated that the variability in spectral accuracy contributed more to the errors than the approximation of the theoretical isotope distribution by our proposed average DNA/RNA model. The prediction model is implemented as an online tool. An R function can be downloaded to incorporate the method in custom analysis workflows to process mass spectral data.

Histopathological Verification of the Diagnostic Performance of the EU-TIRADS Classification of Thyroid Nodules-Results of a Multicenter Study Performed in a Previously Iodine-Deficient Region.

BACKGROUND: To validate the European Thyroid Imaging and Reporting Data System EU-TIRADS classification in a multi-institutional database of thyroid nodules by analyzing the obtained scores and histopathology results. METHODS: A total of 842 thyroid lesions (613 benign, 229 malignant) were identified in 428 patients (mean age 62.7 years) and scored according to EU-TIRADS, using ultrasound examination. In all tumors, histopathological verification was performed. RESULTS: In EU-TIRADS 2 (154 nodules) all nodules were benign; in EU-TIRADS 3, only 3/93 malignancies were identified. In EU-TIRADS 4, 12/103 were malignant, and in EU-TIRADS 5 (278 benign vs. 214 malignant). The malignant nodules that would not have qualified for biopsy were: EU-TIRADS 3, 2/3 (67%) malignancies were <20 mm, in EU-TIRADS 4, 7/12 (58%) were <15 mm. In EU-TIRADS 5, 72/214 (34%) were <10 mm; in total, 81/229 (36%) malignant lesions would have been missed. The cutoff between EU-TIRADS 3/4 had sensitivity of 100%, specificity of 25.1%. Using cutoff for EU-TIRADS 5, 93.4%, 54.6%, respectively. CONCLUSION: The application of EU-TIRADS guidelines allowed us to achieve moderate specificity. The vast majority of malignancies in EU-TIRADS 3, 4, and 5 would not have been recommended for biopsy because having a smaller size than that proposed classification.