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Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples.

Recent advances in mass spectrometry have resulted in deep proteomic analysis along with the generation of robust and reproducible datasets. However, despite the considerable technical advancements, sample preparation from biospecimens such as patient blood, CSF, and tissue still poses considerable challenges. For identifying biomarkers, tissue proteomics often provides an attractive sample source to translate the research findings from the bench to the clinic. It can reveal potential candidate biomarkers for early diagnosis of cancer and neurodegenerative diseases such as Alzheimer's disease,…

Discrimination of Bacillus cereus Group Members by MALDI-TOF Mass Spectrometry.

Matrix-Assisted Laser Desorption/Ionization Time Of Flight Mass Spectrometry (MALDI-TOF MS) technology is currently increasingly used in diagnostic laboratories as a cost effective, rapid and reliable routine technique for the identification and typing of microorganisms. In this study, we used MALDI-TOF MS to analyze a collection of 160 strains belonging to the Bacillus cereus group (57 B. anthracis, 49 B. cereus, 1 B. mycoides, 18 B. wiedmannii, 27 B. thuringiensis, 7 B. toyonensis and 1 B. weihenstephanensis) and to detect specific biomarkers which would allow an unequivocal identification. …

Next-Generation Paternò-Büchi Reagents for Lipid Analysis by Mass Spectrometry.

The Paternò-Büchi (PB) reaction is a photochemical reaction involving [2 + 2] cycloaddition between electronically excited carbonyl and carbon-carbon double bond (C═C). It has been established as a lipid derivatization strategy, leading to confident assignment of C═C locations in lipids when coupled with tandem mass spectrometry (MS/MS). Although acetone and several aryl-containing ketones or aldehydes have been explored as PB reagents, the chemical properties critical to achieving efficient conversion and minimum side reactions remain unclear. Herein, we investigated a set of acetophenone (AP…

Spatially resolved analysis of FFPE tissue proteomes by quantitative mass spectrometry.

Bottom-up mass spectrometry-based proteomics relies on protein digestion and peptide purification. The application of such methods to broadly available clinical samples such as formalin-fixed and paraffin-embedded (FFPE) tissues requires reversal of chemical crosslinking and the removal of reagents that are incompatible with mass spectrometry. Here, we describe in detail a protocol that combines tissue disruption by ultrasonication, heat-induced antigen retrieval and two alternative methods for efficient detergent removal to enable quantitative proteomic analysis of limited amounts of FFPE mat…

Сравнительная последовательность tRNA и масс-спектрометрия РНК для обследования модификаций tRNA.

Химические модификации нуклеозидов, из которых состоят тРНК, являются разнообразными. Однако структура, расположение и степень модификаций были систематически отображены в очень малком числе организмов. Здесь мы описываем подход, в котором быстрая предсказание модифицированных сайтов через обратную транскрипцию-полученные сигнатуры в высокопроизводительных данных тРНК-секвенирования (tRNA-seq) объединяется с идентификацией модификаций тРНК через масс-спектрометрию РНК. Сравнительное тРНК-секвенирование позволило предсказать несколько модификаций Vibrio cholerae, отсутствующих у Escherichia col

Совпадение в аннотации оригинала
Chemical modifications of the nucleosides that comprise transfer RNAs are diverse. However, the structure, location and extent of modificati … fer RNA-sequencing (tRNA-seq) data is coupled with identification of tRNA modifications through RNA mass spectrometry. Comparative tRNA-seq enabled prediction of several Vibrio cholerae modifications that are absent from Escherichia coli and also revealed the effects of various environmental conditions on V. cholerae tRNA modification. Through RNA mass spectrometri …

Serum steroid profiling by mass spectrometry in adrenocortical tumors: diagnostic implications.

PURPOSE OF REVIEW: Liquid chromatography-tandem mass spectrometry (LC-MS/MS), allowing the reliable measurement of large panels of steroids, opened a new era in the characterization of adrenal diseases. This review summarizes the most recent findings on serum steroid profile in benign adrenocortical tumors and provides a focus on the most promising analytical developments. RECENT FINDINGS: Recently developed LC-MS/MS assays included challenging compounds, providing new knowledge on adrenal steroid secretion. Pioneering studies highlighted the potential of incoming technologies in increasing m…

Quantitative Swab Touch Spray Mass Spectrometry for Oral Fluid Drug Testing.

Simultaneous determination of 30 common drugs of abuse, including opioids, benzodiazepines, fentanyl derivatives, methamphetamines, cocaine, substituted methylenedioxyphenethylamines, cathinones, antidepressants, and antipsychotics, in neat oral fluid was carried out using touch spray mass spectrometry from volumetric absorptive microsampling swabs. A simple and rapid (<2 min per sample) method using multiple reaction monitoring was developed and fully validated, yielding satisfactory analytical performance. Minimal sample volumes (10 μL) were used, and neither sample transfer nor preparation …

Selective Gas Chromatography Mass Spectrometry Method for Ultratrace Detection of Selenocyanate.

The recent interest in the determination of selenocyanate (SeCN-) in wastewater systems has spurred the development of analytical methods for its determination at the ultratrace level. Since most of the current procedures require complex and costly instrumental configurations, we have developed a simple and rapid gas chromatography tandem mass spectrometry (GC/MS/MS) method able to detect SeCN- in water samples with a LOD of 0.1 ng/g Se. A 1 mL volume of aqueous sample was buffered with sodium bicarbonate and treated with triethyloxonium tetrafluoroborate for conversion of the analyte into vol…

Gangliosidome of human anencephaly: A high resolution multistage mass spectrometry study.

Widely dispersed throughout the entire body tissues, gangliosides (GGs) are essential components of neuronal cell membranes, where exhibit a … ion of neural development with deficient concentration of several GGs, a systematic and comparative mass spectrometry (MS) mapping assay on GGs originating from fetuses in different intrauterine developmental stages, i.e. the 29th (denoted An29), 35th (An35) and the 37th (An37) gestational weeks was here conducted. Our approach, based on Orbitrap MS under high sens …

Multiplex quantitative imaging of human myocardial infarction by mass spectrometry-immunohistochemistry.

Simultaneous assessment of a panel of protein markers is becoming essential in order to enhance biomarker research and improve diagnostics. Specifically, postmortem diagnostics of early myocardial ischemia in sudden cardiac death cases could benefit from a multiplex marker assessment in the same tissue section. Current analytical antibody-based techniques (immunohistochemistry and immunofluorescence) limit multiplex analysis usually to not more than three antibodies. In this study, mass spectrometry-immunohistochemistry (MS-IHC) was performed by combining laser ablation inductively coupled pla…

Mass spectrometry-based peptidome profiling of human serous ovarian cancer tissues.

BACKGROUND: Bioactive peptides existing in vivo have been considered as an important class of natural medicines for the treatment of diseases. Peptidome analysis of tissues and biofluids had provided important information about the differentially expressed bioactive peptides in vivo. METHODS: Here, we analyzed the peptidome of serous ovarian cancer tissue samples and normal ovarian epithelial tissue samples by mass spectrometry and further investigated the possible bioactive peptides that were differentially expressed. RESULTS: We identified 634 differentially expressed peptides, 508 of thes…

Investigating the Lymphatic System by Dual-Color Elemental Mass Spectrometry Imaging.

Secondary lymphedema accompanied with strong restrictions in quality of life is still major side effects in cancer therapy. Therefore, dedicated diagnostic tools and further investigation of the lymphatic system are crucial to improve lymphedema therapy. In this pilot study, a method for quantitative analysis of the lymphatic system in a rat model by laser ablation (LA) with inductively coupled plasma mass spectrometry imaging (ICP-MSI) is presented. As a possible lymph marker, thulium(III)(1R,4R,7R,10R)-α,α',α'',α'''-tetramethyl-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate (Tm-DOTMA) …

Monitoring chemical changes during food sterilisation using ultrahigh resolution mass spectrometry.

Sterilised food products undergo chemical changes during processing that ultimately determine the product quality. To provide detailed information on the chemistry of each stage of a pet-food sterilisation process, a laboratory-scale system was developed, which allowed sampling under the high temperatures and pressures associated with sterilisation. Products from the laboratory-scale system were representative of the factory process. Sample extracts were analysed by Fourier Transform-Ion Cyclotron Resonance-Mass Spectrometry (FT-ICR-MS), which delivered the molecular formulae and ion intensiti…

Glycan analysis by ion mobility-mass spectrometry and gas-phase spectroscopy.

Due to the existence of numerous isomers, the in-depth analysis of glycans represents a major challenge. Currently, the majority of glycans are analysed using mass spectrometry (MS)-based techniques, which can provide information on regioisomers but usually fail to differentiate stereoisomers. A promising approach to overcome this limitation is to implement ion mobility spectrometry (IMS) as an additional gas-phase separation dimension. This review highlights recent developments in which IM-MS was used as a tool for comprehensive glycan analysis or as rapid screening method for glycan feature …

Selective screening of glutaric acid acidurias by capillary electrophoresis-mass spectrometry.

A sensitive and selective method for the separation and quantification of the three organic acids 3-hydroxy-3-methylglutaric acid, 3-methylglutaric acid, and glutaric acid in human urine samples by CE with mass spectrometry detection has been developed. This methodology is faster, simpler and less time-consuming, than other methodologies previously described, and requires of reduced amounts of reagents as well. Samples are first filtered and then diluted in water. For the electrophoretic separation, a 20mM ammonium acetate and 10% methanol solution at pH 9.1 was selected as the running electro…

Optimization and Validation of High-Resolution Mass Spectrometry Data Analysis Parameters.

High-resolution mass spectrometry (HRMS) has gained recognition as a valuable tool for comprehensive drug screening in a variety of biological matrices. HRMS instruments collect untargeted, accurate mass data, which permit identification of known and unknown compounds in a single analytical run. One of the most challenging aspects of implementing an HRMS drug screen is establishing appropriate data analysis parameters for identifying compounds. Unlike other types of mass spectrometry data, guidelines for HRMS data analysis and acceptability criteria have not been established. Although many lab…

Blind testing of cross-linking/mass spectrometry hybrid methods in CASP11.

Hybrid approaches combine computational methods with experimental data. The information contained in the experimental data can be leveraged to probe the structure of proteins otherwise elusive to computational methods. Compared with computational methods, the structures produced by hybrid methods exhibit some degree of experimental validation. In spite of these advantages, most hybrid methods have not yet been validated in blind tests, hampering their development. Here, we describe the first blind test of a specific cross-link based hybrid method in CASP. This blind test was coordinated by the

Applying liquid chromatography-tandem mass spectrometry to assess endodontic sealer microleakage.

The objective of this study was to describe a new method for the quantitative analysis of a microleakage of endodontic filling materials. Fo … olution was measured after 10, 30, and 60 days, using high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). None of the groups presented microleakage at 10 days. At 30 days, G2 and G3 showed similar infiltration patterns (means: 16.0 and 13.9 ng mL-1, respectively), whereas G1 showed significantly higher values (mean: 105.2 ng mL-1). At 60 d …