Tag: LiP-MS

Abstract Here, we present FLiPPR, or FragPipe LiP (limited proteolysis) Processor, a tool that facilitates the analysis of data from limited proteolysis mass spectrometry (LiP-MS) experiments following primary search and quantification in FragPipe. LiP-MS has emerged as a method that can provide proteome-wide information on protein structure and has been…

Library-free and machine learning-augmented data analysis with Spectronaut® 18 yields industry-leading protein quantification and throughput for DIA proteomics Novel collaborative research using the TrueDiscovery® and TrueTarget® CRO services platforms demonstrates the quantitative precision and wide applicability of mass spectrometry proteomics for biomarker discovery and drug development Biognosys’ iRT Kit is…

Limited proteolysis coupled to mass spectrometry (LiP-MS) is a recent proteomics technique that allows structure-based target engagement profiling on a proteome-wide level. To achieve this, native lysates are first incubated with a compound, followed by a short incubation with a nonspecific protease. Binding of a compound can change accessibility at…

Effective target identification and validation lie at the heart of modern drug discovery. Yet the current repertoire of cancer therapeutics is still focused on a relatively small subset of targets compared with the overall “druggable” biology within cancer cells.   Genetic technologies such as genomics and transcriptomics have opened up…

Spectronaut® 18 makes DIA proteomics projects more efficient and scalable than ever for all mass spectrometry instrument types Novel research with TrueDiscovery™ and TrueTarget™ demonstrates the unique capabilities and utility of mass spectrometry proteomics for biomarker and drug discovery Biognosys’ iRT Kit is recommended for real-time system suitability monitoring in…

In collaboration with prominent biopharma companies and academic institutions, Biognosys will demonstrate the technological advances and versatility of the TrueDiscovery™, TrueTarget™, and TrueSignature™ proteomics platforms across the entire spectrum of oncology research and clinical development Proteoverse™ offers intuitive and interactive data visualization to make proteomics data more accessible and easily…

During drug development, understanding how a compound binds to its target(s) is an important step in lead selection and optimization. A thorough dissection of drug–protein interactions helps to investigate structure-activity relationships and elucidate mechanisms of binding, which set key milestones in compound development.   But this important step is also…

Changes in the structure of 76 proteins in the cerebrospinal fluid (CSF) of people with Parkinson’s disease were seen when compared with those of healthy individuals, a study reported. Its researchers believe their work is the first to look at protein structure — rather than abundance — to identify potential new…

Parkinson’s disease is on the rise as average ages increase, but treatment is often delayed through difficulties in distinguishing its early symptoms from other conditions. The discovery that proteins in a patient’s spinal fluid have distinctive structures could address this problem. It could also increase our understanding of the causes…

This article includes research findings that are yet to be peer-reviewed. Results are therefore regarded as preliminary and should be interpreted as such. Find out about the role of the peer review process in research here. For further information, please contact the cited source. Over the last 20 years, advances…

Overview of protti functions. protti can be used on the output of any software package for quantitative analysis of bottom-up proteomics experiments and provides a flexible set of functions for quality control, as well as data pre-processing, data analysis and data interpretation. Credit: Bioinformatics Advances (2021). DOI: 10.1093/bioadv/vbab041 A recent…

Peptides are mapped onto PDB structures or AlphaFold prediction based on their positions. This is accomplished by replacing the B-factor information in the structure file with values that allow highlighting of peptides, protein regions or amino acids when the structure is coloured by B-factor. In addition to simply highlighting peptides,…