AIMC Topic: Proteomics

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A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes.

Nature communications
Chemoproteomics is a key technology to characterize the mode of action of drugs, as it directly identifies the protein targets of bioactive compounds and aids in the development of optimized small-molecule compounds. Current approaches cannot identif...

A Deep Learning-Based Tumor Classifier Directly Using MS Raw Data.

Proteomics
Since the launch of Chinese Human Proteome Project (CNHPP) and Clinical Proteomic Tumor Analysis Consortium (CPTAC), large-scale mass spectrometry (MS) based proteomic profiling of different kinds of human tumor samples have provided huge amount of v...

Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.

Cell systems
Cancer is driven by genomic alterations, but the processes causing this disease are largely performed by proteins. However, proteins are harder and more expensive to measure than genes and transcripts. To catalyze developments of methods to infer pro...

Aptamer based proteomic pilot study reveals a urine signature indicative of pediatric urinary tract infections.

PloS one
OBJECTIVE: Current urinary tract infection (UTI) diagnostic strategies that rely on leukocyte esterase have limited accuracy. We performed an aptamer-based proteomics pilot study to identify urine protein levels that could differentiate a culture pro...

A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry.

Cytometry. Part A : the journal of the International Society for Analytical Cytology
The application of machine learning and artificial intelligence to high-dimensional cytometry data sets has increasingly become a staple of bioinformatic data analysis over the past decade. This is especially true in the field of cancer biology, wher...

The Age of Data-Driven Proteomics: How Machine Learning Enables Novel Workflows.

Proteomics
A lot of energy in the field of proteomics is dedicated to the application of challenging experimental workflows, which include metaproteomics, proteogenomics, data independent acquisition (DIA), non-specific proteolysis, immunopeptidomics, and open ...

Immunopeptidomic Data Integration to Artificial Neural Networks Enhances Protein-Drug Immunogenicity Prediction.

Frontiers in immunology
Recombinant DNA technology has, in the last decades, contributed to a vast expansion of the use of protein drugs as pharmaceutical agents. However, such biological drugs can lead to the formation of anti-drug antibodies (ADAs) that may result in adve...

An Approach to Biomarker Discovery of Cannabis Use Utilizing Proteomic, Metabolomic, and Lipidomic Analyses.

Cannabis and cannabinoid research
Relatively little is known about the molecular pathways influenced by cannabis use in humans. We used a multi-omics approach to examine protein, metabolomic, and lipid markers in plasma differentiating between cannabis users and nonusers to understa...

MealTime-MS: A Machine Learning-Guided Real-Time Mass Spectrometry Analysis for Protein Identification and Efficient Dynamic Exclusion.

Journal of the American Society for Mass Spectrometry
Mass spectrometry-based proteomics technologies are prime methods for the high-throughput identification of proteins in complex biological samples. Nevertheless, there are still technical limitations that hinder the ability of mass spectrometry to id...