Related papers: De novo peptide sequencing rescoring and FDR estim…
De novo peptide sequencing is a critical task in proteomics. However, the performance of current deep learning-based methods is limited by the inherent complexity of mass spectrometry data and the heterogeneous distribution of noise…
The discovery of novel proteins relies on sensitive protein identification, for which de novo peptide sequencing (DNPS) from mass spectra is a crucial approach. While deep learning has advanced DNPS, existing models inadequately enforce the…
De novo peptide sequencing from mass spectrometry data is an important method for protein identification. Recently, various deep learning approaches were applied for de novo peptide sequencing and DeepNovoV2 is one of the represetative…
Motivation: Accurate estimation of false discovery rate (FDR) of spectral identification is a central problem in mass spectrometry-based proteomics. Over the past two decades, target decoy approaches (TDAs) and decoy-free approaches (DFAs),…
Proteins are the main workhorses of biological functions in a cell, a tissue, or an organism. Identification and quantification of proteins in a given sample, e.g. a cell type under normal/disease conditions, are fundamental tasks for the…
De novo peptide sequencing algorithms have been widely used in proteomics to analyse tandem mass spectra (MS/MS) and assign them to peptides, but quality-control methods to evaluate the confidence of de novo peptide sequencing are lagging…
Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning methods have been developed for \emph{de novo} peptide…
Proteomics is the large-scale analysis of the proteins. The common method for identifying proteins and characterising their amino acid sequences is to digest the proteins into peptides, analyse the peptides using mass spectrometry and…
De novo peptide sequencing is a fundamental computational technique for ascertaining amino acid sequences of peptides directly from tandem mass spectrometry data, eliminating the need for reference databases. Cutting-edge models usually…
De novo peptide sequencing aims to recover amino acid sequences of a peptide from tandem mass spectrometry (MS) data. Existing approaches for de novo analysis enumerate MS evidence for all amino acid classes during inference. It leads to…
Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based proteomics is a well-established research field with major applications such as identification of disease biomarkers, drug discovery, drug design and development. In…
Peptide de novo sequencing is a method used to reconstruct amino acid sequences from tandem mass spectrometry data without relying on existing protein sequence databases. Traditional deep learning approaches, such as Casanovo, mainly…
Motivation: Target-decoy search (TDS) is currently the most popular strategy for estimating and controlling the false discovery rate (FDR) of peptide identifications in mass spectrometry-based shotgun proteomics. While this strategy is very…
Tandem mass spectrometry (MS/MS) stands as the predominant high-throughput technique for comprehensively analyzing protein content within biological samples. This methodology is a cornerstone driving the advancement of proteomics. In recent…
Most deep noise suppression (DNS) models are trained with reference-based losses requiring access to clean speech. However, sometimes an additive microphone model is insufficient for real-world applications. Accordingly, ways to use real…
Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences…
Speech enhancement employing deep neural networks (DNNs) for denoising are called deep noise suppression (DNS). During training, DNS methods are typically trained with mean squared error (MSE) type loss functions, which do not guarantee…
Personalized cancer vaccines are envisioned as the next generation rational cancer immunotherapy. The key step in developing personalized therapeutic cancer vaccines is to identify tumor-specific neoantigens that are on the surface of tumor…
Metaproteomics are becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS)…
Physics-informed neural networks (PINNs) have recently emerged as an alternative way of solving partial differential equations (PDEs) without the need of building elaborate grids, instead, using a straightforward implementation. In…