相关论文: Open Mass Spectrometry Search Algorithm

Metabolomics complements investigation of the genome, transcriptome, and proteome of an organism. Today, the vast majority of metabolites remain unknown, in particular for non-model organisms. Mass spectrometry is one of the predominant…

Protein structure similarity search (PSSS), which tries to search proteins with similar structures, plays a crucial role across diverse domains from drug design to protein function prediction and molecular evolution. Traditional…

Peptide identification in mass spectrometry-based proteomics is crucial for understanding protein function and dynamics. Traditional database search methods, though widely used, rely on heuristic scoring functions and statistical…

Addressing the issue of SVMs parameters optimization, this study proposes an efficient memetic algorithm based on Particle Swarm Optimization algorithm (PSO) and Pattern Search (PS). In the proposed memetic algorithm, PSO is responsible for…

This paper proposes a novel Extended Particle Swarm Optimization model (EPSO) that potentially enhances the search process of PSO for optimization problem. Evidently, gene expression profiles are significantly important measurement factor…

Most current sampling algorithms for high-dimensional distributions are based on MCMC techniques and are approximate in the sense that they are valid only asymptotically. Rejection sampling, on the other hand, produces valid samples, but is…

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…

We introduce an alternative formulation of the exact stochastic simulation algorithm (SSA) for sampling trajectories of the chemical master equation for a well-stirred system of coupled chemical reactions. Our formulation is based on…

Similarity search in math is to find mathematical expressions that are similar to a user's query. We conceptualized the similarity factors between mathematical expressions, and proposed an approach to math similarity search (MSS) by…

Mass spectrometry is the dominant technology in the field of proteomics, enabling high-throughput analysis of the protein content of complex biological samples. Due to the complexity of the instrumentation and resulting data, sophisticated…

Mass spectrometry is a widely used method to study molecules and processes in medicine, life sciences, chemistry, catalysis, and industrial product quality control, among many other applications. One of the main features of some mass…

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of…

Crosslinking mass spectrometry (Crosslinking MS) has substantially matured as a method over the last two decades through parallel development in multiple labs, demonstrating its applicability for protein structure determination,…

Statistical models for proteomics data often estimate protein fold changes between two samples, A and B, as the average peptide intensity from sample A divided by the average peptide intensity from sample B. Such average intensity ratios…

The ensemble average of physical properties of molecules is closely related to the distribution of molecular conformations, and sampling such distributions is a fundamental challenge in physics and chemistry. Traditional methods like…

Feature selection for predictive analytics is the problem of identifying a minimal-size subset of features that is maximally predictive of an outcome of interest. To apply to molecular data, feature selection algorithms need to be scalable…

Crosslinking Mass Spectrometry (MS) can uncover protein-protein interactions and provide structural information on proteins in their native cellular environments. Despite its promise, the field remains hampered by inconsistent data formats,…

Ordinary differential equations (ODE) are widely used for modeling in Systems Biology. As most commonly only some of the kinetic parameters are measurable or precisely known, parameter estimation techniques are applied to parametrize the…

Searches for new particles often span a wide range of mass scales, where the shape of potential signals and the SM background varies significantly. We make use of a multivariate method that fully exploits the correlation between signal and…

As the structural databases continue to expand, efficient methods are required to search similar structures of the query structure from the database. There are many previous works about comparing protein 3D structures and scanning the…