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Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics
Journal of Proteome Research. 2015. Vol. 14. No. 8. P. 3148–3161.
Interpreting the potentially vast number of hypotheses generated by a shotgun proteomics experiment requires a valid and accurate procedure for assigning statistical confidence estimates to the identified tandem mass spectra. Despite the crucial role such procedures play in most highthroughput proteomics experiments, the scientific literature has not reached a consensus about the best confidence estimation methodology. In this work, we evaluate, using theoretical and empirical analysis, four previously proposed protocols for estimating the false discovery rate (FDR) associated with a set of identified tandem mass spectra: two variants of the target-decoy competition protocol (TDC) of Elias and Gygi and two variants of the separate target-decoy search protocol of Kall et al. Our analysis reveals signi ficant biases in the two separate target-decoy search protocols. Moreover, the one of the TDC protocol that provides an unbiased estimate FDR among the target PSMs does so at the cost of forfeiting a random subset of high-scoring spectrum identifications. We therefore propose the mix-max procedure to provide unbiased, accurate FDR estimates in the presence of a well-calibrated scores. The method avoids biases associated with the two separate target-decoy search protocols and also avoids the propensity for target-decoy competition to discard a random subset of high-scoring target identifications
Piontkovski D., / Series arXiv "math". 2026.
A noncommutative projective variety is defined, following Artin and Zhang, by a graded coherent algebra 𝐴. The category of coherent sheaves is then the quotient qgr(𝐴) of the category of finitely presented graded modules by the subcategory of torsion modules. We consider the categorical and polynomial entropies of the Serre twist, that is, of the ...
Added: June 23, 2026
Piontkovski D., / Series arXiv "math". 2025.
If a symmetric multilinear algebra is weakly nil, then it is Engel. This result may be regarded as an infinite-dimensional analogue of the well-known Jacobian theorem, which states that if a polynomial mapping has a polynomial inverse, then its Jacobian matrix is invertible. This refines a theorem of Gerstenhaber and partially answers a question posed ...
Added: June 23, 2026
Shipilov F., Barnyakov A., Ivanov A. et al., / Series Physics "arxiv.org". 2026.
A fast simulation of the detector response is a vital task in high-energy physics (HEP). Traditional Monte-Carlo methods form the backbone of modern particle physics simulation software but are computationally expensive. We present a machine-learning-based approach to fast simulation of the Focusing Aerogel Ring Imaging Cherenkov (FARICH) detector response. Given a particle track and momentum, ...
Added: May 19, 2026
Derkacheva A., Sakirkina M., Kraev G. et al., /. 2026.
Comprehensive data on natural hazards and their consequences are crucial for effective for risk assessment, adaptation planning, and emergency response. However, many countries face challenges with fragmented, inconsistent, and inaccessible data, particularly regarding local-scale events. To address this data gap in Russia, we developed an end-to-end processing pipeline that scrapes news from various online sources, ...
Added: April 28, 2026
Pilé I., Deng Y., Shchur L., / Series arXiv "math". 2026. No. 2604.10254.
We investigate the spatial overlap of successive spin configurations in Markov chain Monte Carlo simulations using the local Metropolis algorithm and the Svendsen-Wang and Wolff cluster algorithms. We examine the dynamics of these algorithms for two models in different universality classes: the Ising model and the Potts model with three components. The overlap of two ...
Added: April 20, 2026
Gabdullin N., Androsov I., / Series Computer Science "arxiv.org". 2026.
Label prediction in neural networks (NNs) has O(n) complexity proportional to the number of classes. This holds true for classification using fully connected layers and cosine similarity with some set of class prototypes. In this paper we show that if NN latent space (LS) geometry is known and possesses specific properties, label prediction complexity can ...
Added: April 2, 2026
Petrova D., Biomolecules 2025
Added: January 18, 2026
Sorokin K., Beketov M., Онучин А. et al., / arxiv.org. Серия cs.SI "Social and Information Networks ". 2025.
Community detection in complex networks is a fundamental problem, open to new approaches in various scientific settings. We introduce a novel community detection method, based on Ricci flow on graphs. Our technique iteratively updates edge weights (their metric lengths) according to their (combinatorial) Foster version of Ricci curvature computed from effective resistance distance between the ...
Added: January 15, 2026
Petrovanov I., Sergeev A., / Series Computer Science "arxiv.org". 2025. No. 2512.18332.
Transport coding reduces message delay in packet-switched networks by introducing controlled redundancy at the transport layer: original packets are encoded into coded packets, and the message is reconstructed after the first successful deliveries, effectively shifting latency from the maximum packet delay to the -th order statistic. We present a concise, reproducible discrete-event implementation of transport coding in OMNeT++, including ...
Added: December 24, 2025
Hessian-based lightweight neural network for brain vessel segmentation on a minimal training dataset
Меньшиков И. А., Бернадотт А. К., Elvimov N. S., / Series arXie "Statistical mechanics". 2025.
Accurate segmentation of blood vessels in brain magnetic resonance angiography (MRA) is essential for successful surgical procedures, such as aneurysm repair or bypass surgery. Currently, annotation is primarily performed through manual segmentation or classical methods, such as the Frangi filter, which often lack sufficient accuracy. Neural networks have emerged as powerful tools for medical image ...
Added: December 1, 2025
Rubchinskiy A., Chubarova D., / Series WP7 "Математические методы анализа решений в экономике, бизнесе и политике". 2025. No. WP7/2025/01.
The article examines one of the most famous examples of socio-economic systems, characterized by significant uncertainty – the S&P-500 stock market, where shares of 500 largest US companies are traded. No assumptions are made about the probabilistic characteristics of the stock market. A flexible algorithm for daily trading has been developed, based on both known fixed data ...
Added: November 9, 2025
Blokhin V., Shupik M., Gutner U. et al., Biomolecules 2022 Vol. 12 No. 1 Article 93
Parkinson’s disease (PD) is a neurodegenerative disease incurable due to late diagnosis and treatment. Therefore, one of the priorities of neurology is to study the mechanisms of PD pathogenesis at the preclinical and early clinical stages. Given the important role of sphingolipids in the pathogenesis of neurodegenerative diseases, we aimed to analyze the gene expression ...
Added: March 4, 2024
V. A. Kalyagin, A. P. Koldanov, P. A. Koldanov, Physica A: Statistical Mechanics and its Applications 2022 Vol. 599 Article 127482
Maximum spanning tree is a popular tool in market network analysis. Large number of publications are devoted to the maximum spanning tree calculation and its interpretation for particular stock markets. Usually one use market data to calculate Pearson correlations between stock returns and construct a compete weighted graph, where weights of edges are given by ...
Added: May 18, 2022
Danilova Yulia, Voronkova Anastasia, Sulimov Pavel et al., Journal of Proteome Research 2019 Vol. 18 No. 5 P. 2354–2358
Accurate target-decoy-based false discovery rate (FDR) control of peptide identification from tandem mass-spectrometry data relies on an important but often neglected assumption that incorrect spectrum annotations are equally likely to receive either target or decoy peptides. Here we argue that this assumption is often violated in practice, even by popular methods. Preference can be given ...
Added: October 6, 2021
Sulimov P., Voronkova A. V., Kertész-Farkas A., Bioinformatics 2020 Vol. 36 No. 12 P. 3781–3787
Motivation
The discrimination ability of score functions to separate correct from incorrect peptide-spectrum-matches in database-searching-based spectrum identification is hindered by many superfluous peaks belonging to unexpected fragmentation ions or by the lacking peaks of anticipated fragmentation ions.
Results
Here, we present a new method, called BoltzMatch, to learn score functions using a particular stochastic neural networks, called restricted ...
Added: August 31, 2020
Sulimov P., Kertesz-Farkas A., Journal of Proteome Research 2020 No. 19(4) P. 1481–1490
Peptide-spectrum-match (PSM) scores used in database searching are calibrated to spectrum- or spectrum-peptide-specific null distributions. Some calibration methods rely on specific assumptions and use analytical models (e.g., binomial distributions), whereas other methods utilize exact empirical null distributions. The former may be inaccurate because of unjustified assumptions, while the latter are accurate, albeit computationally exhaustive. Here, ...
Added: June 29, 2020
Ovchinnikova K., Lachlan S., Rakhlin A. et al., Bioinformatics 2020 P. 1–10
Motivation
Imaging mass spectrometry (imaging MS) is a prominent technique for capturing distributions of molecules in tissue sections. Various computational methods for imaging MS rely on quantifying spatial correlations between ion images, referred to as co-localization. However, no comprehensive evaluation of co-localization measures has ever been performed; this leads to arbitrary choices and hinders method development.
Results
We ...
Added: March 15, 2020
Vladimir A. Korshun, Analytical Methods 2017 Vol. 9 No. 45 P. 6335–6340
The derivatization reagent was prepared in situ by the reaction of tris(2,6-dimethoxyphenyl)methylium hexafluorophosphate with N-(2- aminoethyl)maleimide and used for the modification of a number of low molecular weight thiols. The adducts were analyzed by (MA)(NA) LDI MS and ESI MS. All registered mass spectra ((MA)(NA)LDI, ESI) revealed intense peaks of the cations of the derivatization products. The increment of the derivatization agent ...
Added: November 8, 2019
Petushkova N., Zgoda V., Pyatnitskiy M. et al., Plos One 2017 Vol. 12 No. 5 P. 0177427-1–0177427-21
Liquid chromatography-tandem mass spectrometry was used to analyze plasma proteins of volunteers (control) and patients with glioblastoma multiform (GBM). A database search was pre-set with a variable post-translational modification (PTM): phosphorylation, acetylation or ubiquitination. There were no significant differences between the control and the GBM groups regarding the number of protein identifications, sequence coverage or number of PTMs. However, in GBM plasma, we unambiguously observed a decreased fraction in post-translationally modified peptides ...
Added: March 14, 2018
Kuznetsova K., Trufanov P., Moysa A. et al., Rapid Communications in Mass Spectrometry 2016 Vol. 30 No. 11 P. 1323–1331
One of the problems in proteogenomic research aimed at identification of variant peptides is the presence of peptides with amino acid isomers of different origin in the analyzed samples. Among the most challenging examples are peptides with threonine and isothreonine (homoserine) in their sequences. Indeed, the latter residue may appear in vitro as a methionine substitution during sample preparation for shotgun proteome analysis. Yet, this substitution of ...
Added: March 14, 2018
Palmer A., Phapale P., Chernyavsky I. et al., Nature Methods 2017 No. 14 P. 57–60
High-mass-resolution imaging mass spectrometry promises to localize hundreds of metabolites in tissues, cell cultures, and agar plates with cellular resolution, but it is hampered by the lack of bioinformatics tools for automated metabolite identification. We report pySM, a framework for false discovery rate (FDR)-controlled metabolite annotation at the level of the molecular sum formula, for ...
Added: February 7, 2017
Kertesz-Farkas A., Myers M. P., Current Bioinformatics 2012 Vol. 7 No. 2 P. 221–230
Bottom-up proteomics (mass spectrometry analysis of peptides obtained by proteolysis and separated by liquid chromatography, (LCMS/MS)) is one of the most frequently used techniques for identifying and characterizing proteins in biological samples. A key element of the analysis is database searching when the mass spectra of the peptides are compared with a database of theoretically ...
Added: November 18, 2015
Kertesz-Farkas A., Grant C. E., Howbert J. J. et al., Journal of Proteome Research 2014 Vol. 13 No. 10 P. 4488–4491
Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit (http://cruxtoolkit.sourceforge.net) is an open source project that aims to provide users with a crossplatform suite of analysis tools for interpreting protein mass spectrometry data. ...
Added: November 18, 2015
Kertesz-Farkas A., Myers M. P., Protein and peptide letters 2014 Vol. 21 No. 8 P. 858–863
Identification and elimination of noise peaks in mass spectra from large proteomics data streams simultaneously improves the accuracy of peptide identification and significantly decreases the size of the data. There are a number of peak filtering strategies that can achieve this goal. Here we present a simple algorithm wherein the number of highest intensity peaks ...
Added: November 18, 2015