Label-free LC-MS methods are attractive for high-throughput quantitative proteomics, as the sample processing is straightforward and can be scaled to a large number of samples. Label-free methods therefore facilitate biomarker discovery in studies involving dozens of clinical samples. However, despite the increased popularity of label-free workflows, there is a hesitance in the research communi...

Synthetic cathinones have recently emerged as a substitute for common drugs of abuse. Synthetic cathinones can elicit powerful adverse effects such as delusions, hallucinations and potentially dangerous behavior. To develop a method to analyze 10 synthetic cathinones in oral fluid, we implemented a combined approach of solid-phase extraction and ultra-high-performance liquid chromatography-tand...

In this paper we develop a Bayesian statistical inference approach to the unified analysis of isobaric labelled MS/MS proteomic data across multiple experiments. An explicit probabilistic model of the log-intensity of the isobaric labels' reporter ions across multiple pre-defined groups and experiments is developed. This is then used to develop a full Bayesian statistical methodology for the id...

Nowadays, proteomics is recognized as one of the fastest growing tools in many areas of research. This is especially true for the study of Saccharomyces cerevisiae, as it is considered to be a model organism for eukaryotic cells. Proteomic analysis provides an insight into global protein expressions from identification to quantitation, from localization to function, and from individual to netwo...

Negative-ion electrospray ionisation mass spectrometry with an anionic phosphine ligand enables detection of key intermediates in the Sonogashira reaction. MS/MS techniques are used to generate a Hammett plot for the key reductive elimination step.

BACKGROUND The endocannabinoid 2-arachidonoyl glycerol (2-AG) undergoes spontaneous isomerization to biologically inactive 1-AG. This effect has not been adequately addressed in previous studies that reported 2-AG concentrations in biological samples. METHODS Liquid chromatography tandem-mass spectrometry (LC-MS/MS) was used for 1-AG and 2-AG analyses. RESULTS Identical collision-induced di...

While prefractionation has previously been shown to improve results in MS analysis, a novel combination provides an additional dimension of separation: protein fractionation by SDS-PAGE followed by IEF of tryptic peptides before separation by RP-LC [Atanassov and Urlaub, Proteomics 2013, 13, 2947-2955]. This three-step separation procedure prior to MS/MS substantially increases proteome coverag...

Time-consuming and experience-dependent manual validations of tandem mass spectra are usually applied to SEQUEST results. This inefficient method has become a significant bottleneck for MS/MS data processing. Here we introduce a program AMASS (advanced mass spectrum screener), which can filter the tandem mass spectra of SEQUEST results by measuring the match percentage of high-abundant ions and...

Mitochondria in a live HepG2 cell were visualized with a fluorescent probe to specify their location and state in a living cell. Then, mitochondria were selectively captured with a nanospray tip under fluorescence microscope, and thousands of small molecular peaks were revealed and unique steroids specific to mitochondria were also found. This fluorescence imaging combined with live single-cell...