The accurate processing of complex liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) data from biological samples is a major challenge for metabolomics, proteomics, and related approaches. Here, we present the pipelines systems threshold-avoiding quantification (PASTAQ) LC–MS/MS preprocessing toolset, which allows highly data-dependent acquisition datasets. PASTAQ performs co...

Understanding protein–ligand interactions in a cellular context is an important goal molecular biology and biochemistry, particularly for drug development. Investigators must demonstrate that drugs penetrate cells specifically bind their targets. Towards end, we present native mass spectrometry (MS)-based method analyzing uptake target engagement eukaryotic cells. This based on our previously i...

Urine is a metabolite-rich biofluid that reflects the body's effort to maintain chemical and osmotic homeostasis. Clinical diagnosis routinely relies on urine samples because the collection process is easy and noninvasive. Despite these advantages, urine is an under-investigated source of biomarkers for multiple sclerosis (MS). Nuclear magnetic resonance spectroscopy (NMR) has become a common a...

BACKGROUND AND OBJECTIVES Multiple Sclerosis (MS) is a chronic recurrent neurological disease that affects the Central Nervous System. This study aims to determine epidemiological factors that affect the appearance of MS, such as: incidence, prevalence, mortality, case appearance in accordance with the disease phase RRMS, SPMS, PPMS, gender, age, age group, and EDSS. MATERIALS AND METHODS Dea...

Endosufan, alpha and beta, and three conversion products, sulphate, ether and lactone, were simultaneously determined in human serum by means of an analytical procedure which combines extraction with organic solvents, clean-up with H(2)SO(4) and by liquid column chromatography, and detection by gas chromatography (GC) using electron capture detection (ECD) and tandem mass spectrometry (MS/MS). ...

In an effort to measure vitamin D, ultra-high-performance liquid chromatography with tandem mass spectrometry (UHPLC-MS/MS) was applied to samples. The use of UHPLC-MS/MS decreased the run time by 50%. The UHPLC-MS/MS achieved equal or better separation efficiency with complex food matrixes compared to HPLC-MS/MS. It was also observed that under the optimized conditions of UHPLC, all previtamin...

BACKGROUND IL-2 receptor (IL2R) alpha is the specific component of the high affinity IL2R system involved in the immune response and in the control of autoimmunity. METHODS AND RESULTS Here we perform a replication and fine mapping of the IL2RA gene region analyzing 3 SNPs previously associated with multiple sclerosis (MS) and 5 SNPs associated with type 1 diabetes (T1D) in a collection of 79...

Efficient strategies are required to implement comprehensive suspect screening methods using high-resolution mass spectrometry within environmental monitoring campaigns. In this study, both liquid and gas chromatography time-of-flight mass spectrometry (LC-QTOF-MS and GC-QTOF-MS) were used to screen for >5000 target and suspect compounds in the Sacramento-San Joaquin River Delta in Northern Cal...

A high-throughput approach for biomolecule analysis is demonstrated for a mixture of peptides from tryptic digest of four proteins as well as a tryptic digests of human plasma. In this method a chip based electrospray autosampler coupled to a hybrid ion mobility (IMS) mass spectrometer (MS) is utilized to achieve rapid sample analysis. This high-throughput measurement is realized by exploiting ...

Current limitations in proteome analysis by high-throughput mass spectrometry (MS) approaches have sometimes led to incomplete (or inconclusive) data sets being published or unpublished. In this work, we used an iTRAQ reference data on hepatocellular carcinoma (HCC) to design a two-stage functional analysis pipeline to widen and improve the proteome coverage and, subsequently, to unveil the mol...