Biology subjects

Baraboshkin, N. M.

Publications and source records attributed to Baraboshkin, N. M..

4 recordsLinked to original sources

bioRxiv2026

Affordable 96-parallel SPPS: hardware and software add-on for automated liquid handling platforms

ParSynt-P is a hardware and software add-on that converts a liquid-handling robot already available in a proteomics laboratory (Tecan Freedom EVO) into a parallel plate-format peptide synthesizer for generating libraries of candidate peptide standards for targeted blood plasma proteomics. The manifold is milled from polytetrafluoroethylene and has ports for an inert gas and a vacuum line; a standard commercially available 96-well filtration plate is secured to it with an airtight seal. The software layer generates robot worklists from a table of peptide sequences and controls switching of the N?/vacuum lines, including pulsed gas mixing. The system performs up to 96 syntheses per run, and coupling of one residue takes 94 min. Workability of this 96-well format was verified on three fully loaded plates. The uniformity of synthesis conversion across the plate was measured quantitatively using a characterized NAT/SIL standard pair. The add-on cost $351, while the synthesis cost is $0.23 per coupling and $1.14 per milligram of crude product, an order of magnitude below the market price of custom synthesis.

biochemistry↗

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↗