AIMC Topic: Mass Spectrometry

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Biological Function Assignment across Taxonomic Levels in Mass-Spectrometry-Based Metaproteomics via a Modified Expectation Maximization Algorithm.

Journal of proteome research
A major challenge in mass-spectrometry-based metaproteomics is accurately identifying and quantifying biological functions across the full taxonomic lineage of microorganisms. This issue stems from what we refer to as the "shared confidently identifi...

Evaluation of the False Discovery Rate in Library-Free Search by DIA-NN Using Human Proteome.

Journal of proteome research
Recently, deep-learning-based spectral libraries have gained increasing attention. Several data-independent acquisition (DIA) software tools have integrated this feature, known as a library-free search, thereby making DIA analysis more accessible. H...

Machine Learning-Based Retention Time Prediction Tool for Routine LC-MS Data Analysis.

Journal of chemical information and modeling
Accurate retention time () prediction models can significantly improve liquid chromatography-mass spectrometry (LC-MS) data analysis widely used in chemical synthesis. As hundreds of thousands of syntheses are performed annually at Enamine, a large a...

Machine Learning-Assisted Iterative Screening for Efficient Detection of Drug Discovery Starting Points.

Journal of medicinal chemistry
High-throughput screening (HTS) remains central to small molecule lead discovery, but increasing assay complexity challenges the screening of large compound libraries. While retrospective studies have assessed active-learning-guided screening, extens...

Measurement and prediction of small molecule retention by Gram-negative bacteria based on a large-scale LC/MS screen.

Scientific reports
The challenge of assessing intracellular accumulation represents a major hurdle to the discovery of new antibiotics with Gram-negative activity. To address this, a high-throughput assay was developed to measure compound uptake and retention in Escher...

Analysis of Protein-Protein Interactions in CC125 by Co-Fractionation Mass Spectrometry.

Journal of proteome research
, a unicellular eukaryotic green alga, is an important biological model. Previous studies on protein complexes in have primarily focused on photosynthesis and ciliary movement, while understanding the overall protein complex network is still limited...

MAMSI: Integration of Multiassay Liquid Chromatography-Mass Spectrometry Metabolomics Data Using Multiview Machine Learning.

Analytical chemistry
Liquid chromatography-mass spectrometry (LC-MS) is a commonly used analytical technique in untargeted metabolomics. However, the diverse chemical and physical properties of metabolites often require the use of several different analytical assays for ...

State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor.

Journal of chemical information and modeling
Accurately resolving a three-dimensional structure that corresponds to an experimental mass spectrometry (MS) result is valuable for outcomes such as improved analyte identification, determination of physiochemical properties relating to conformation...

Simultaneous determination of 7 thiols associated proteins in lymphoma patients'serum and cerebrospinal fluid by UHPLC-HRMS technique.

Scientific reports
Thiol compounds can serve as markers for the antioxidant and prognostic status of lymphoma, playing a crucial role in early tumor diagnosis. However, their high polarity and lack of chromophores pose challenges for multivariate analysis. This study a...

A novel UHPLC-HRMS method for simultaneous determination of 20 amino metabolites and proteins in lymphoma patients' cells and serum.

Scientific reports
Highly sensitive and selective monitoring of amino metabolites such as glutamine, arginine, tryptophan and related proteins played significant roles in early diagnosis and warning of lymphoma. But those limited abundance and lacked chromophore group ...