Biology subjects

Fedorov, O. V.

Publications and source records attributed to Fedorov, O. V..

4 recordsLinked to original sources

bioRxiv2026

Direct empirical in-house assessment of peptide proteotypicity for targeted proteomics

In bottom-up proteomics peptide it was early shown that despite a certain protein is present in a sample, only a subset of its proteolytic peptide products will be detected with LC-MS analysis. Property of peptide being frequently detected given its source proteins identification was called proteotypicity. Much effort has been since applied to predict proteotypic peptides and summarize evidence on peptide detection. Nevertheless, when targeted proteomics method is being developed, prediction or inference from communal experience might be inaccurate and prior knowledge of true peptide proteotypicity in a selected setup for a selected population is necessary. In this work we test fully in-house approach for proteotypicity assessment including comprehensive peptide synthesis and detection verification. Proteotypicity and contribution of sample processing and biology-related factors are estimated in a model experiment for three plasma proteins, albumin, ceruloplasmin and C-reactive protein.

genomics↗

bioRxiv2026

Quality control of blood plasma for mass-spectrometry proteomic research

Mishandling of samples during blood plasma preparation may lead to biases in proteomic analysis and false interpretation of data. Previous plasma proteome profiling study (Geyer, Mann et al., 2019) described proteins that may serve to indicate poor plasma sample quality. We have established a targeted quantitative method for three prominent panels of markers proposed by previous study for exclusion of hemolyzed and coagulation samples. We conducted a model experiment similar to Geyer, Mann et al., with both panoramic and targeted detection and investigated the feasibility of application internal control for hemolysis in targeted proteomic analysis by using incorrectly collected plasma. We propose to include plasma sample hemolysis assessment into standard MRM analysis and associated sample exclusion criteria.

systems biology↗

bioRxiv2026

Addressing diagnostic gaps in thyroid pathology: a multiplex protein panel as an adjunctive tool for risk stratification and differentiation of thyroid neoplasms

Fine-needle aspiration biopsy of thyroid nodules frequently yields indeterminate results, leading to unnecessary diagnostic surgeries. We evaluated a targeted plasma proteomics approach to differentiate benign follicular thyroid adenoma (FTA) from malignant papillary thyroid carcinoma (PTC). Using LC-MRM mass spectrometry with stable isotope-labeled standards (SIS), we quantified a multiplex protein panel in plasma samples from 267 patients. The analytical workflow incorporated an MS-based assessment of preanalytical hemolysis to prevent bias associated with thyroid-related blood composition changes and multiple rounds of randomization allowed assessment of batch effects. While previously proposed low-abundance thyroid cancer markers were rarely detected in the cohort, a signature of high-abundance plasma proteins successfully stratified the patients. The malignant PTC phenotype was characterized by a significant increase in apolipoprotein A1 and myosin-9, along with elevated CD14 and kininogen-1. Benign FTA was associated with higher levels of acute-phase proteins, including ceruloplasmin and complement C1q subunit C. Simple PCRE model with 20 parameters based on 4 major plasma proteins allowed to build a classifier with specificity that can be adjusted with regard to epidemiology and medical resource. This study establishes a foundational mass spectrometry-based framework that utilizes systemic proteomic profiles to differentiate underlying pathologies and improve clinical decision-making regarding patient management. By enabling additional stratification of patients with Bethesda IV cytology, who are otherwise frequently subjected to unwarranted diagnostic operations, this multiplex MS approach provides a potential non-invasive triage tool to reduce unnecessary surgical interventions for indeterminate thyroid nodules.

systems biology↗

bioRxiv2019

Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum

The archaellum is a unique motility structure that has only functional similarity to its bacterial counterpart, the flagellum. Archaellar filaments consist of thousands of copies of the protein protomer archaellin. Most euryarchaeal genomes encode multiple homologous archaellins. The role of these multiple archaellin genes remains unclear. Halophilic archaea from the genus Halorubrum possess two archaellin genes, flaB1 and flaB2. Amino acid sequences of the corresponding protein products are extraordinarily diverged (identity of [~] 40%). To clarify roles for each archaellin, we compared archaella from two natural Halorubrum lacusprofundi strains: the DL18 strain, which possesses both archaellin genes, and the type strain ACAM 34 whose genome contains the flaB2 gene only. Both strains synthesize functional archaella; however, the DL18 strain, where both archaellins are present in comparable amounts, is more motile. In addition, we expressed these different Hrr. lacusprofundi archaellins in a Haloferax volcanii strain from which the endogenous archaellin genes were deleted. Three Hfx. volcanii strains expressing Hrr. lacusprofundi archaellins flaB1, flaB2 or flaB1-flaB2 produced archaellum filaments consisting of only one (FlaB1 or FlaB2) or both (FlaB1/B2) archaellins. All three recombinant Hfx. volcanii strains were motile, although there were profound differences in the efficiency of motility. The recombinant filaments resemble the natural filaments of Hrr. lacusprofundi. Electron microscopy showed that FlaB1 FlaB2-archaella look like typical supercoiled filaments, while with the shape of the FlaB1- and FlaB2-archaella is more variable. Both native and recombinant FlaB1 FlaB2-filaments have greater thermal stability and are more resistant to low salinity stress than single-component filaments. This shows that thermal stability of archaellins depends on the presence of both archaellin types, indicating a close interaction between these subunits in the supramolecular structure. Functional helical Hrr. lacusprofundi archaella can be composed of either single archaellin: FlaB2 or FlaB1; however, the two divergent archaellin subunits in combination provide additional stabilization to the archaellum structure and thus adaptation to a wider range of external conditions. A comparative genomic analysis of archaellins suggests that the described combination of divergent archaellins is not restricted to Hrr. lacusprofundi, but is occurring also in organisms from other haloarchaeal genera.

microbiology↗