Spectral library
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To address the lack of high-resolution electron ionisation mass spectral libraries (HR-[EI+]-MS) for environmental chemicals, a retention-indexed HR-[EI+]-MS library has been constructed following analysis of authentic compounds via GC-Orbitrap MS. The library is freely provided alongside a compound database of predicted physicochemical properties. Currently, the library contains over 350 compounds from 56 compound classes and includes a range of legacy and emerging contaminants. The RECETOX Exposome HR-[EI+]-MS library expands the number of freely available resources for use in full-scan chemical exposure studies and is available at: https://doi.org/10.5281/zenodo.4471217.
Renal cell carcinoma (RCC) represents 2.2% of all cancer incidences; however, prognostic or predictive RCC biomarkers at protein level are largely missing. To support proteomics research of localized and metastatic RCC, we introduce a new library of targeted mass spectrometry assays for accurate protein quantification in malignant and normal kidney tissue. Aliquots of 86 initially localized RCC, 75 metastatic RCC and 17 adjacent non-cancerous fresh frozen tissue lysates were trypsin digested, pooled, and fractionated using hydrophilic chromatography. The fractions were analyzed using LC-MS/MS on QExactive HF-X mass spectrometer in data-dependent acquisition (DDA) mode. A resulting spectral library contains 77,817 peptides representing 7960 protein groups (FDR = 1%). Further, we confirm applicability of this library on four RCC datasets measured in data-independent acquisition (DIA) mode, demonstrating a specific quantification of a substantially increased part of RCC proteome, depending on LC-MS/MS instrumentation. Impact of sample specificity of the library on the results of targeted DIA data extraction was demonstrated by parallel analyses of two datasets by two pan human libraries. The new RCC specific library has potential to contribute to better understanding the RCC development at molecular level, leading to new diagnostic and therapeutic targets.
Východiská: Kvantifikácia proteínov v modelových nádorových bunečných líniách a v nádorových tkanivách je často predmetom onkologického výskumu. Metóda SWATH (sequential windowed acquisition of all theoretical fragment ion spectra), novinka v kvantitatívnej onkoproteomike, získava čoraz väčšiu popularitu, pretože umožňuje kvantifikáciu všetkých proteínov zaznamenaných v spektrálnej knižnici. Spektrálna knižnica obsahuje fragmentačné informácie o každom detekovateľnom proteíne vo vzorke. Dôkladná príprava spektrálnej knižnice výrazne vylepší kvantifikáciu obzvlášť nízkoabundantných proteínov, ktoré často zohrávajú výnamnú úlohu v nádorových ochoreniach. Cieľ: V tomto článku sa venujeme optimalizácii prípravy spektrálnej knižnice s cieľom maximalizovať počet kvantifikovateľných proteínov v modelovej bunečnej línii MCF-7 odvodenej od karcinómu prsníka. Experiment je zameraný na optimalizáciu postupu prípravy vzorky pred vstupom do hmotnostného spektrometru, kde bol skúmaný vplyv zloženia lyzačného pufru, vplyv postupu rozpúšťania peptidov a vplyv materiálu mikroskúmaviek na počet proteínov v spektrálnej knižnici. V neposlednom rade boli optimalizované aj parametre merania na hmotnostnom spektrometri pre získavanie dát do spektrálnej knižnice. Záver: Dôslednou optimalizáciou postupu sa podarilo pripraviť spektrálnu knižnicu obsahujúcu fragmentačné informácie o 1 653 proteínoch (FDR < 1%) z 1 ?g lyzátu MCF-7. Hlavným prínosom optimalizácie postupu prípravy spektrálnej knižnice je rozšírenie pokrytia proteómu vo SWATH digitálnych biobankách umožňujúcich kvantifikáciu ľubovoľného proteínu vo fyzicky už nedostupných vzorkách. Kvalitné spektrálne knižnice by mohli v budúcnosti zohrávať kľúčovú úlohu pri tvorbe digitálnych fingerprintov proteómu pacientov.
Background: Cancer research often focuses on protein quantication in model cancer cell lines and cancer tissues. SWATH (sequential windowed acquisition of all theoretical fragment ion spectra), the state of the art method, enables the quantication of all proteins included in spectral library. Spectral library contains fragmentation patterns of each detectable protein in a sample. Thorough spectr
- Klíčová slova
- digitální biobanka, SWATH,
- MeSH
- hmotnostní spektrometrie * metody využití MeSH
- lidé MeSH
- nádorové biomarkery * analýza chemie MeSH
- proteiny analýza chemie MeSH
- proteomika metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
In the case of a release of highly pathogenic bacteria (HPB), there is an urgent need for rapid, accurate, and reliable diagnostics. MALDI-TOF mass spectrometry is a rapid, accurate, and relatively inexpensive technique that is becoming increasingly important in microbiological diagnostics to complement classical microbiology, PCR, and genotyping of HPB. In the present study, the results of a joint exercise with 11 partner institutions from nine European countries are presented. In this exercise, 10 distinct microbial samples, among them five HPB, Bacillus anthracis, Brucella canis, Burkholderia mallei, Burkholderia pseudomallei, and Yersinia pestis, were characterized under blinded conditions. Microbial strains were inactivated by high-dose gamma irradiation before shipment. Preparatory investigations ensured that this type of inactivation induced only subtle spectral changes with negligible influence on the quality of the diagnosis. Furthermore, pilot tests on nonpathogenic strains were systematically conducted to ensure the suitability of sample preparation and to optimize and standardize the workflow for microbial identification. The analysis of the microbial mass spectra was carried out by the individual laboratories on the basis of spectral libraries available on site. All mass spectra were also tested against an in-house HPB library at the Robert Koch Institute (RKI). The averaged identification accuracy was 77% in the first case and improved to >93% when the spectral diagnoses were obtained on the basis of the RKI library. The compilation of complete and comprehensive databases with spectra from a broad strain collection is therefore considered of paramount importance for accurate microbial identification.
- MeSH
- Bacteria chemie klasifikace MeSH
- bakteriologické techniky metody MeSH
- mezinárodní spolupráce MeSH
- spektrometrie hmotnostní - ionizace laserem za účasti matrice metody MeSH
- testování odbornosti laboratoří * MeSH
- Publikační typ
- časopisecké články MeSH
- multicentrická studie MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
Peptide spectral libraries enable targeted identification and quantitation of low-abundance proteins in a complex plant proteome. Here we describe parallel protein and peptide fractionation techniques to improve plant proteome coverage and facilitate construction of spectral libraries.
Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.
- MeSH
- hmotnostní spektrometrie metody MeSH
- internet MeSH
- ionty chemie metabolismus MeSH
- metabolické sítě a dráhy * MeSH
- metabolomika metody MeSH
- molekulární struktura MeSH
- reprodukovatelnost výsledků MeSH
- software MeSH
- výpočetní biologie metody MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
The potential of mMass software search tool with new compound libraries was demonstrated on metabolomics of Scedosporium prolificans, S. apiospermum and Pseudallescheria boydii sensu stricto. Cyclic peptides pseudacyclins, small molecular weight tyroscherin analogues and various lipids were annotated by public software tool (http://www.mmass.org) utilising accurate matrix-assisted laser desorption/ionisation mass spectral data of intact fungal spores. Electrospray ionisation combined with tandem mass spectrometry was used for monohexosylceramide characterisation in fungal extracts.
Mass spectrometry raw data repositories, including Metabolomics Workbench and MetaboLights, have contributed to increased transparency in metabolomics studies and the discovery of novel insights in biology by reanalysis with updated computational metabolomics tools. Herein, we reanalyzed the previously published lipidomics data from nine algal species, resulting in the annotation of 1437 lipids achieving a 40% increase in annotation compared to the previous results. Specifically, diacylglyceryl-carboxyhydroxy-methylcholine (DGCC) in Pavlova lutheri and Pleurochrysis carterae, glucuronosyldiacylglycerol (GlcADG) in Euglena gracilis, and P. carterae, phosphatidylmethanol (PMeOH) in E. gracilis, and several oxidized phospholipids (oxidized phosphatidylcholine, OxPC; phosphatidylethanolamine, OxPE; phosphatidylglycerol, OxPG; phosphatidylinositol, OxPI) in Chlorella variabilis were newly characterized with the enriched lipid spectral databases. Moreover, we integrated the data from untargeted and targeted analyses from data independent tandem mass spectrometry (DIA-MS/MS) acquisition, specifically the sequential window acquisition of all theoretical fragment-ion MS/MS (SWATH-MS/MS) spectra, to increase the lipidomic annotation coverage. After the creation of a global library of precursor and diagnostic ions of lipids by the MS-DIAL untargeted analysis, the co-eluted DIA-MS/MS spectra were resolved in MRMPROBS targeted analysis by tracing the specific product ions involved in acyl chain compositions. Our results indicated that the metabolite quantifications based on DIA-MS/MS chromatograms were somewhat inferior to the MS1-centric quantifications, while the annotation coverage outperformed those of the untargeted analysis of the data dependent and DIA-MS/MS data. Consequently, integrated analyses of untargeted and targeted approaches are necessary to extract the maximum amount of metabolome information, and our results showcase the value of data repositories for the discovery of novel insights in lipid biology.
- Publikační typ
- časopisecké články MeSH
BACKGROUND: The emergence of psychoactive designer drugs has significantly increased over the last few years. Customs officials are responsible for the control of products entering the European Union (EU) market. This control applies to chemicals in general, pharmaceutical products and medicines. Numerous products imported from non-EU countries, often declared as 'bath salts' or 'fertilizers', contain new psychoactive substance (NPS). REVIEW: These are not necessarily controlled under international law, but may be subject to monitoring in agreement with EU legislation. This situation imposes substantial challenges, for example, for the maintenance of spectral libraries used for their detection by designated laboratories. The chemical identification of new substances, with the use of powerful instrumentation, and the time needed for detailed analysis and interpretation of the results, demands considerable commitment. The EU Joint Research Centre endeavors to provide scientific support to EU Customs laboratories to facilitate rapid identification and characterisation of seized samples. In addition to analysing known NPS, several new chemical entities have also been identified. Frequently, these belong to NPS classes already notified to the European Monitoring Centre for Drugs and Drug Addiction (EMCDDA) by the European Early- Warning System (EWS). CONCLUSION: The aim of this paper is to discuss the implementation of workflow mechanisms that are in place in order to facilitate the monitoring, communication and management of analytical data. The rapid dissemination of this information between control authorities strives to help protect EU citizens against the health risks posed by harmful substances.
