AIMC Topic: Mass Spectrometry

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UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines.

BMC systems biology
BACKGROUND: The conjugation of ubiquitin to a substrate protein (protein ubiquitylation), which involves a sequential process--E1 activation, E2 conjugation and E3 ligation, is crucial to the regulation of protein function and activity in eukaryotes....

Analytical approach to determining human biogenic amines and their metabolites using eVol microextraction in packed syringe coupled to liquid chromatography mass spectrometry method with hydrophilic interaction chromatography column.

Talanta
Analysis of biogenic amines (BAs) in different human samples provides insight into the mechanisms of various biological processes, including pathological conditions, and thus may be very important in diagnosing and monitoring several neurological dis...

Liquid chromatography quadrupole time-of-flight mass spectrometry selective determination of ochratoxin A in wine.

Food chemistry
The performance of liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) for ochratoxin A (OTA) determination in wine is evaluated for the first time. Sample preparation was optimized to obtain quantitative recoveries at the ...

A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs.

BMC bioinformatics
Protein O-GlcNAcylation, involving the β-attachment of single N-acetylglucosamine (GlcNAc) to the hydroxyl group of serine or threonine residues, is an O-linked glycosylation catalyzed by O-GlcNAc transferase (OGT). Molecular level investigation of t...

Illuminating the dark matter in metabolomics.

Proceedings of the National Academy of Sciences of the United States of America

Gradient liquid chromatographic retention time prediction for suspect screening applications: A critical assessment of a generalised artificial neural network-based approach across 10 multi-residue reversed-phase analytical methods.

Talanta
For the first time, the performance of a generalised artificial neural network (ANN) approach for the prediction of 2492 chromatographic retention times (tR) is presented for a total of 1117 chemically diverse compounds present in a range of complex ...

Searching molecular structure databases with tandem mass spectra using CSI:FingerID.

Proceedings of the National Academy of Sciences of the United States of America
Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually rely on tandem MS to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. ...

l2 Multiple Kernel Fuzzy SVM-Based Data Fusion for Improving Peptide Identification.

IEEE/ACM transactions on computational biology and bioinformatics
SEQUEST is a database-searching engine, which calculates the correlation score between observed spectrum and theoretical spectrum deduced from protein sequences stored in a flat text file, even though it is not a relational and object-oriental reposi...

The SwissLipids knowledgebase for lipid biology.

Bioinformatics (Oxford, England)
MOTIVATION: Lipids are a large and diverse group of biological molecules with roles in membrane formation, energy storage and signaling. Cellular lipidomes may contain tens of thousands of structures, a staggering degree of complexity whose significa...