相关论文: PUB-MS - a mass-spectrometry-based method to monit…

Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used,…

Proteins congregate into complexes to perform fundamental cellular functions. Phenotypic outcomes, in health and disease, are often mechanistically driven by the remodeling of protein complexes by protein coding mutations or cellular…

Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins…

Mass spectrometry provides a high-throughput approach to identify proteins in biological samples. A key step in the analysis of mass spectrometry data is to identify the peptide sequence that, most probably, gave rise to each observed…

Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in a sample are first broken into their constituent peptides. The resulting mixture of peptides is then subjected…

Biological processes rely on finely tuned homo- and heteromeric interactions between (biomacro)molecules. The strength of an interaction, typically given by the dissociation constant (KD), plays a crucial role in basic research and must be…

Mass spectrometry (MS) is used widely in biomolecular structural analysis and is particularly dominant in the study of proteins. Despite its considerable power, state-of-the-art protein MS frequently suffers from limited reliability 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,…

Protein footprinting is a new methodology that is based on probing, typically with the use of mass spectrometry, of reactivity of different aminoacid residues to a modifying reagent. Data thus obtained allow one to make inferences about…

The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an…

We propose a novel method for template matching in unconstrained environments. Its essence is the Best-Buddies Similarity (BBS), a useful, robust, and parameter-free similarity measure between two sets of points. BBS is based on counting…

Motivation: Mass spectrometry-based proteomics is among the most commonly used methods for scrutinizing proteomic profiles in different organs for biological or medical researches. All the proteomic analyses including peptide/protein…

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,…

Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules. This larger number of molecules and the associated larger dynamic range have major implications in the development of proteomics technologies. We examine…

Analyzing the kinetics of biological processes plays a significant role in understanding fundamental cellular functions. Many physics-based technologies used to study such processes are limited by the shot noise inherent to the coherent…

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…

Sequence coverage in MS analysis of protein digestion-derived peptides is a key issue for detailed characterization of proteins or identification at low quantities. In gel-based proteomics studies, the sequence coverage greatly depends on…

Protein-ligand binding affinity (PLBA) prediction is the fundamental task in drug discovery. Recently, various deep learning-based models predict binding affinity by incorporating the three-dimensional structure of protein-ligand complexes…

The ultimate target of proteomics identification is to identify and quantify the protein in the organism. Mass spectrometry (MS) based on label-free protein quantitation has mainly focused on analysis of peptide spectral counts and ion peak…

Protein interaction networks (PIN) are popular means to visualize the proteome. However, PIN datasets are known to be noisy, incomplete and biased by the experimental protocols used to detect protein interactions. This paper aims at…