AIMC Topic: Proteomics

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Proteomics coupled machine learning-innovative approach in geographical origin authentication of green Coffea arabica.

Food chemistry
The geographical authentication of green specialty coffee is an economically sensitive analytical task that is not yet fully resolved. We used an innovative combination of proteomic profiling with linear discriminant analysis for the authentication o...

Off-site processing of data-dependent and data-independent acquisition shotgun proteomics data with MASSyPupX.

Journal of proteomics
The rapid pace of shotgun proteomics data generation presents challenges for timely data analysis. In parallel, the scientific community is creating novel data interpretation tools, such as artificial intelligence, that have not yet been integrated i...

Plasma proteomics for biomarker discovery in childhood tuberculosis.

Nature communications
Failure to rapidly diagnose tuberculosis disease (TB) and initiate treatment is a driving factor of TB as a leading cause of death in children. Current TB diagnostic assays have poor performance in children, thus a global priority is the identificati...

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...

A perspective on integrating digital pathology, proteomics, clinical data and AI analytics in cancer research.

Journal of proteomics
Nearly 40 % of individuals will be diagnosed with cancer in their lifetime, translating to an estimated 20 million new cases annually. Despite remarkable therapeutic advances, only 15-20 % of patients achieve durable responses to immunotherapy, and t...

Library-based virtual match-between-runs quantification in GlyPep-Quant improves site-specific glycan identification.

Nature communications
Glycosylation changes are closely related to various diseases, including cancer. The quantitative analysis of site-specific glycans at proteomics scale remains challenging due to low glycopeptide spectra interpretation. Here, we present GlyPep-Quant,...

AZGP1: A proteomic biomarker in cancer.

Clinica chimica acta; international journal of clinical chemistry
Alpha-2-glycoprotein 1, zinc-binding (AZGP1), functions as a serum AZGP1 biomarker with applications in cancer detection, prognosis, and therapeutic monitoring. This review evaluates AZGP1's analytical performance and clinical utility in multiple mal...

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...

Machine Learning and DIA Proteomics Reveal New Insights into Carbapenem Resistance Mechanisms in .

Journal of proteome research
The emergence of Carbapenem-resistant (CRKP) represents a major public health concern, primarily driven by its ability to evade a wide range of antibiotics. Despite extensive genomic studies, proteomic insights into antibiotic resistance mechanisms ...