Cross-linking mass spectrometry (MS) has substantially matured as a method over the past 2 decades through parallel development in multiple labs, demonstrating its applicability to protein structure determination, conformation analysis, and mapping protein interactions in complex mixtures. Cross-linking MS has become a much-appreciated and routinely applied tool, especially in structural biology. Therefore, it is timely that the community commits to the development of methodological and reporting standards. This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Cross-linking MS for which guidelines should be developed as part of a Cross-linking MS standards initiative.
- MeSH
- hmotnostní spektrometrie přístrojové vybavení metody normy MeSH
- konformace proteinů MeSH
- lidé MeSH
- mapování interakce mezi proteiny metody MeSH
- mezinárodní spolupráce MeSH
- proteiny ultrastruktura MeSH
- proteomika přístrojové vybavení metody normy MeSH
- reagencia zkříženě vázaná chemie MeSH
- reprodukovatelnost výsledků MeSH
- směrnice jako téma MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- kongresy MeSH
- práce podpořená grantem MeSH
Hydrogen/deuterium exchange monitored by mass spectrometry is a promising technique for rapidly fingerprinting structural and dynamical properties of proteins. The time-dependent change in the mass of any fragment of the polypeptide chain depends uniquely on the rate of exchange of its amide hydrogens, but determining the latter from the former is generally not possible. Here, we show that, if time-resolved measurements are available for a number of overlapping peptides that cover the whole sequence, rate constants for each amide hydrogen exchange (or equivalently, their protection factors) may be extracted and the uniqueness of the solutions obtained depending on the degree of peptide overlap. However, in most cases, the solution is not unique, and multiple alternatives must be considered. We provide a statistical method that clusters the solutions to further reduce their number. Such analysis always provides meaningful constraints on protection factors and can be used in situations in which obtaining more refined experimental data is impractical. It also provides a systematic way to improve data collection strategies to obtain unambiguous information at single-residue level (e.g., for assessing protein structure predictions at atomistic level).
The androgens dehydroepiandrosterone sulfate, dehydro-epiandrosterone, androstenedione and testosterone are routinely assessed in women, and circulating levels of these androgens reflect their production. These androgens are measured in most laboratories using various immuno-analytical methods. Recently, however, androgen assays have begun to be performed using gas or liquid chromatography combined with mass spectrometry. To better understand the difficulties and issues of androgen laboratory diagnostics, it is important to assess each of the methods used, how and why they were introduced into practice, and their advantages, limits, historic milestones and current status. It is also necessary to understand how reference ranges are determined and specifics arising from the physiology of individual androgens. Here we present a summary and discussion of these issues.
- MeSH
- androgeny krev MeSH
- androstendion krev MeSH
- biologické markery krev MeSH
- chromatografie kapalinová normy MeSH
- dehydroepiandrosteron krev MeSH
- hmotnostní spektrometrie normy MeSH
- lidé MeSH
- nemoci endokrinního systému krev diagnóza MeSH
- referenční hodnoty MeSH
- testosteron krev MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- přehledy MeSH
The term precision of a value describes the total number of significant digits that are used to express that value. False precision is presented in data, where the sampling and chosen data file format coding return values with extra non-valid digits. The proper precision in value thus depends on so-called magnitude in digital data coding. The presence of the false precision is file format dependent. The amount of dataset points could be decreased by removing false precision (where it is present) to almost 10% of the raw measurement without loss of information.
Phosphatidylcholine (PC) species in human plasma are used as biomarkers of disease. PC biomarkers are often limited by the inability to separate isobaric PCs. In this work, we developed a targeted shotgun approach for analysis of isobaric and isomeric PCs. This approach is comprised of two MS methods: a precursor ion scanning (PIS) of mass m/z 184 in positive mode (PIS m/z +184) and MS(3) fragmentation in negative mode, both performed on the same instrument, a hybrid triple quadrupole ion-trap mass spectrometer. The MS(3) experiment identified the FA composition and the relative abundance of isobaric and sn-1, sn-2 positional isomeric PC species, which were subsequently combined with absolute quantitative data obtained by PIS m/z +184 scan. This approach was applied to the analysis of a National Institute of Standards and Technology human blood plasma standard reference material (SRM 1950). We quantified more than 70 PCs and confirmed that a majority are present in isobaric and isomeric mixtures. The FA content determined by this method was comparable to that obtained using GC with flame ionization detection, supporting the quantitative nature of this MS method. This methodology will provide more in-depth biomarker information for clinical and mechanistic studies.
- MeSH
- biologické markery analýza krev MeSH
- fosfatidylcholiny krev izolace a purifikace MeSH
- hmotnostní spektrometrie metody normy MeSH
- lidé MeSH
- referenční standardy MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Mucin-1 kidney disease, previously described as medullary cystic kidney disease type 1 (MCKD1, OMIM 174000), is an autosomal dominant tubulointerstitial kidney disease recently shown to be caused by a single-base insertion within the variable number tandem repeat region of the MUC1 gene. Because of variable age of disease onset and often subtle signs and symptoms, clinical diagnosis of mucin-1 kidney disease and differentiation from other forms of hereditary kidney disease have been difficult. The causal insertion resides in a variable number tandem repeat region with high GC content, which has made detection by standard next-generation sequencing impossible to date. The inherently difficult nature of this mutation required an alternative method for routine detection and clinical diagnosis of the disease. We therefore developed and validated a mass spectrometry-based probe extension assay with a series of internal controls to detect the insertion event using 24 previously characterized positive samples from patients with mucin-1 kidney disease and 24 control samples known to be wild type for the variant. Validation results indicate an accurate and reliable test for clinically establishing the molecular diagnosis of mucin-1 kidney disease with 100% sensitivity and specificity across 275 tests called.
- MeSH
- diagnostické techniky molekulární * MeSH
- genotyp MeSH
- hmotnostní spektrometrie metody normy MeSH
- lidé MeSH
- mucin 1 genetika MeSH
- mutace * MeSH
- polycystické ledviny autozomálně dominantní diagnóza genetika MeSH
- průběh práce MeSH
- reprodukovatelnost výsledků MeSH
- senzitivita a specificita MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
V súčasnosti je často diskutovanou témou problematika zneužívania drog u mladistvých. Počet požiadaviek na vyšetrenie drog zo strany lekárov, ale aj rodičov počas posledných rokov narastá a úmerne tomu rastie aj počet pozitívnych nálezov. Popri „tradičných“ drogách bol na východnom Slovensku zaznamenaný výskyt nových psychoaktívnych látok. Cieľom tejto práce bolo informovať o výskyte dvoch syntetických látok desoxypipradrole (2-difenylmetylpiperidín, 2-DPMP) a α-pyrolidinovalerofenóne (alfa-PVP) vo východoslovenskom regióne a štatisticky zhodnotiť výsledky našich analýz za obdobie rokov 2012 – 2014. Tiež sme chceli porovnať údaje o úžívaní týchto drog s „tradičnými“ drogami ako sú marihuana, amfetamíny, opiáty a kokaín. Súbor vzoriek tvorili pacienti z psychiatrických ambulancií a z Centra pre liečbu drogových závislostí (CPLDZ) v Košiciach. Vzorky pacientov boli do laboratória posielané v rámci rutinného toxikologického vyšetrenia na zistenie prítomnosti drog a iných zneužívaných liečiv. Analýzy na zistenie prítomnosti nových psychoaktívnych látok boli robené na vysoko citlivých chromatografických prístrojoch GCMS a LCMSMS. Tieto metódy boli vybrané ako spoľahlivé na identifikáciu pôvodnej formy, ako aj metabolitov týchto látok. Viac ako 80 % chromatografických analýz (z celkového počtu 4996) realizovaných v rokoch 2012 – 2014 bolo cielených na odhalenie užívania nezákonnych látok. Z výsledkov analýz vyplýva, že drogou číslo jeden na východe Slovenska je stále marihuana. Novým fenoménom medzi drogami sú novšie psychostimulanciá, ktorých predaj je častokrát maskovaný. Vo východoslovenskom regióne bol zaznamenaný od začiatku roka 2012 výskyt dvoch psychostimulancií, a to 2-DPMP a alfa-PVP.
Currently, one of the most discussed topic is the problem of drug abuse in adolescents. The number of requests for investigation of drugs by doctors, as well as parents increases over the years and is growing in proportion to the number of positive findings. In addition to „traditional“ drugs, the emergence of new psychoactive substances has been recorded in eastern Slovakia. The aim of this work is to provide information on the presence of two synthetic substances desoxypipradrol (2-diphenylmethylpiperidine, 2-DPMP) and α-pyrrolidinovalerophenone (alpha-PVP) in the eastern region of Slovakia and statistically evaluate the results of our analysis for the period 2012-2014, and compare data on the use of these drugs with „traditional“ drugs such as marijuana, amphetamines, opiates and cocaine. Samples were collected from psychiatric clinics and the Center for Treatment of Drug Addiction (CTDD) in Košice. Patient samples were sent to our laboratory under routine toxicological testing for the presence of drugs and other abused drugs. The presence of new psychoactive substances was determined using a highly sensitive chromatography techniques – GCMS and LCMSMS. These methods were selected as reliable for the identification of the original form of the drugs and their metabolites. More than 80 % chromatographic analyses (of total 4996) were performed for the purpose of detection of illicit substances over the years 2012 to 2014. Analysis has shown that the number one drug in eastern Slovakia is marijuana. A new phenomenon among new drugs are stimulants, the sale of which is often masked. Since the beginning of 2012 the incidence of two psychostimulants, 2-DPMP and alpha-PVP has been observed.
- Klíčová slova
- desoxypipradrol, alfa-pyrolidinovalerofenon, toxikologická analýza, tradiční drogy,
- MeSH
- chromatografie kapalinová metody normy přístrojové vybavení MeSH
- chromatografie plynová metody normy přístrojové vybavení MeSH
- hmotnostní spektrometrie metody normy přístrojové vybavení MeSH
- lidé MeSH
- mladiství MeSH
- odhalování abúzu drog metody přístrojové vybavení využití MeSH
- piperidiny * aplikace a dávkování izolace a purifikace moč škodlivé účinky MeSH
- poruchy spojené s užíváním psychoaktivních látek * diagnóza klasifikace prevence a kontrola terapie MeSH
- uživatelé drog * klasifikace statistika a číselné údaje MeSH
- Check Tag
- lidé MeSH
- mladiství MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Geografické názvy
- Slovenská republika MeSH
Celiac disease is a food intolerance triggered by the ingestion of gluten-containing cereals; the only therapy is a strict gluten-free diet for life. In recent years, gluten-free cereal bars has achieved considerable attention as an interesting alternative food considering its several advantages, such as functional properties, nutritional contents, variety of presentations and flavors. The aim of this study was to determine the contents of three toxic trace elements (arsenic, cadmium and lead) in commercial gluten-free cereal bars marketed in Argentina by ICP-MS and assess the dietary intake of the three toxic elements compared with reference values. The results obtained indicated that the highest total concentration of arsenic is provided by the gluten-free cereal bars with green apple pomace (28.2 µg/kg) and the levels of cadmium were lower than 10 µg/kg or even below MDL in all samples. The lead contents in all bars with honey samples were exceptionally higher than in the other samples (levels greater than 130 µg/kg). The intake of available gluten-free cereal bars are generally safe for consumers, but particular attention should be paid to monitor the content of arsenic and lead gluten-free cereal bars to ensure the quality of the product. Further studies are necessary to achieve an exact risk evaluation, concerning the bioavailability of trace elements in gluten-free food sources.
- MeSH
- analýza potravin * metody normy pracovní síly statistika a číselné údaje MeSH
- arsen analýza izolace a purifikace toxicita MeSH
- bezlepková dieta * MeSH
- celiakie * diagnóza dietoterapie imunologie komplikace prevence a kontrola MeSH
- hmotnostní spektrometrie metody normy přístrojové vybavení statistika a číselné údaje MeSH
- hodnocení rizik * MeSH
- hodnotící studie jako téma * MeSH
- kadmium analýza izolace a purifikace toxicita MeSH
- kvalita jídla MeSH
- lidé * MeSH
- olovo analýza izolace a purifikace toxicita MeSH
- potraviny pro zvláštní výživu * analýza statistika a číselné údaje toxicita MeSH
- stopové prvky analýza MeSH
- Check Tag
- lidé * MeSH
- Publikační typ
- práce podpořená grantem MeSH
- Geografické názvy
- Argentina MeSH
A method for identification of highly fluorescent compounds in vine leaves infected by Plasmopara viticola was developed using reversed phase liquid chromatography with simultaneous diode array and fluorometric detection. Fluorescent compounds were extracted from leaves with a methanol-water mixture (70:30). Separation by HPLC was performed using a C(18) column and gradient elution with water-acetonitrile mixtures (20-80% of acetonitrile). The main unknown fluorescent compound was identified by line spectral comparison with a standard obtained by UV photoisomerization of trans-resveratrol glucoside, and its structure was confirmed by liquid chromatography-mass spectrometry. Identification and structural elucidation of the fluorescent compound in the leaves of Vitis vinifera allows early detection of Plasmopara viticola invasion.
- MeSH
- chromatografie kapalinová normy MeSH
- fenantreny chemie izolace a purifikace MeSH
- fluorescenční barviva chemie izolace a purifikace MeSH
- glukosidy chemie izolace a purifikace účinky záření MeSH
- hmotnostní spektrometrie normy MeSH
- isomerie MeSH
- listy rostlin chemie metabolismus mikrobiologie MeSH
- nemoci rostlin mikrobiologie MeSH
- Peronospora MeSH
- referenční standardy MeSH
- rostlinné extrakty chemie izolace a purifikace MeSH
- stilbeny chemie účinky záření MeSH
- ultrafialové záření MeSH
- Vitis chemie metabolismus mikrobiologie MeSH
- vysokoúčinná kapalinová chromatografie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Sphingolipid ceramide N-deacylase (SCDase, EC 3.5.1.69) is a hydrolytic enzyme isolated from Pseudomonas sp. TK 4. In addition to its primary deacylation function, this enzyme is able to reacylate lyso-sphingolipids under specific conditions. We immobilised this enzyme on magnetic macroporous cellulose and used it to semisynthesise C17:0 glucosylceramide and C17:0 sulphatide, which are required internal standards for quantification of the corresponding glycosphingolipids (GSL) by tandem mass spectrometry. A high rate of conversion was achieved for both lipids (80% for C17:0 sulphatide and 90% for C17:0 glucosylceramide). In contrast to synthesis with a soluble form of the enzyme, use of immobilised SCDase significantly reduced the contamination of the sphingolipid products with other isoforms, so further purification was not necessary. Our method can be effectively used for the simple preparation of specifically labelled sphingolipids of high isoform purity for application in mass spectrometry.
- MeSH
- amidohydrolasy chemie MeSH
- bakteriální proteiny chemie MeSH
- enzymy imobilizované chemie MeSH
- glukosylceramidy chemická syntéza chemie MeSH
- glykosfingolipidy analýza MeSH
- hmotnostní spektrometrie metody normy MeSH
- hydrolýza MeSH
- Pseudomonas enzymologie MeSH
- referenční standardy MeSH
- stereoizomerie MeSH
- sulfoglykosfingolipidy chemická syntéza chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
