scholarly journals Revisiting Five Years of CASMI Contests with EPA Identification Tools

Metabolites ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 260
Author(s):  
Andrew D. McEachran ◽  
Alex Chao ◽  
Hussein Al-Ghoul ◽  
Charles Lowe ◽  
Christopher Grulke ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution Mass Spectrometry ◽  
Critical Assessment ◽  
Tandem Mass ◽  
Chemical Identification ◽  
Compound Identification ◽  
Software Applications ◽  
Targeted Analysis ◽  
The Us ◽  
Fit For Purpose

Software applications for high resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) continue to enhance chemical identification capabilities. Given the variety of available applications, determining the most fit-for-purpose tools and workflows can be difficult. The Critical Assessment of Small Molecule Identification (CASMI) contests were initiated in 2012 to provide a means to evaluate compound identification tools on a standardized set of blinded tandem mass spectrometry (MS/MS) data. Five CASMI contests have resulted in recommendations, publications, and invaluable datasets for practitioners of HRMS-based screening studies. The US Environmental Protection Agency’s (EPA) CompTox Chemicals Dashboard is now recognized as a valuable resource for compound identification in NTA studies. However, this application was too new and immature in functionality to participate in the five previous CASMI contests. In this work, we performed compound identification on all five CASMI contest datasets using Dashboard tools and data in order to critically evaluate Dashboard performance relative to that of other applications. CASMI data was accessed via the CASMI webpage and processed for use in our spectral matching and identification workflow. Relative to applications used by former contest participants, our tools, data, and workflow performed well, placing more challenge compounds in the top five of ranked candidates than did the winners of three contest years and tying in a fourth. In addition, we conducted an in-depth review of the CASMI structure sets and made these reviewed sets available via the Dashboard. Our results suggest that Dashboard data and tools would enhance chemical identification capabilities for practitioners of HRMS-based NTA.

scholarly journals Benchmarking Non-Targeted Metabolomics Using Yeast-Derived Libraries

Metabolites ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 160
Author(s):  
Evelyn Rampler ◽  
Gerrit Hermann ◽  
Gerlinde Grabmann ◽  
Yasin El Abiead ◽  
Harald Schoeny ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Quality Control ◽  
Protein Identification ◽  
Regulatory Elements ◽  
Yeast Fermentation ◽  
Compound Identification ◽  
Targeted Metabolomics ◽  
Targeted Analysis ◽  
Orthogonal State ◽  
Starting Point

Non-targeted analysis by high-resolution mass spectrometry (HRMS) is an essential discovery tool in metabolomics. To date, standardization and validation remain a challenge. Community-wide accepted cost-effective benchmark materials are lacking. In this work, we propose yeast (Pichia pastoris) extracts derived from fully controlled fermentations for this purpose. We established an open-source metabolite library of >200 identified metabolites based on compound identification by accurate mass, matching retention times, and MS/MS, as well as a comprehensive literature search. The library includes metabolites from the classes of (1) organic acids and derivatives (2) nucleosides, nucleotides, and analogs, (3) lipids and lipid-like molecules, (4) organic oxygen compounds, (5) organoheterocyclic compounds, (6) organic nitrogen compounds, and (7) benzoids at expected concentrations ranges of sub-nM to µM. As yeast is a eukaryotic organism, key regulatory elements are highly conserved between yeast and all annotated metabolites were also reported in the human metabolome database (HMDB). Orthogonal state-of-the-art reversed-phase (RP-) and hydrophilic interaction chromatography mass spectrometry (HILIC-MS) non-targeted analysis and authentic standards revealed that 104 out of the 206 confirmed metabolites were reproducibly recovered and stable over the course of three years when stored at −80 °C. Overall, 67 out of these 104 metabolites were identified with comparably stable areas over all three yeast fermentation and are the ideal starting point for benchmarking experiments. The provided yeast benchmark material enabled not only to test for the chemical space and coverage upon method implementation and developments but also allowed in-house routines for instrumental performance tests. Transferring the quality control strategy of proteomics workflows based on the number of protein identification in HeLa extracts, metabolite IDs in the yeast benchmarking material can be used as metabolomics quality control. Finally, the benchmark material opens new avenues for batch-to-batch corrections in large-scale non-targeted metabolomics studies.

scholarly journals National Academy of Clinical Biochemistry Laboratory Medicine Practice Guidelines: Follow-Up Testing for Metabolic Disease Identified by Expanded Newborn Screening Using Tandem Mass Spectrometry; Executive Summary

2009 ◽  
Vol 55 (9) ◽  
pp. 1615-1626 ◽  
Author(s):  
Dennis J Dietzen ◽  
Piero Rinaldo ◽  
Ronald J Whitley ◽  
William J Rhead ◽  
W Harry Hannon ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Tandem Mass Spectrometry ◽  
Organic Acids ◽  
Newborn Screening ◽  
Tandem Mass ◽  
Confirmatory Testing ◽  
The Us ◽  
The Impact

Abstract Background: Almost all newborns in the US are screened at birth for multiple inborn errors of metabolism using tandem mass spectrometry. Screening tests are designed to be sufficiently sensitive so that cases are not missed. The NACB recognized a need for standard guidelines for laboratory confirmation of a positive newborn screen such that all babies would benefit from equal and optimal follow-up by confirmatory testing. Methods: A committee was formed to review available data pertaining to confirmatory testing. The committee evaluated previously published guidelines, published methodological and clinical studies, clinical case reports, and expert opinion to support optimal confirmatory testing. Grading was based on guidelines adopted from criteria derived from the US Preventive Services Task Force and on the strength of recommendations and the quality of the evidence. Three primary methods of analyte measurement were evaluated for confirmatory testing including measurement of amino acids, organic acids, and carnitine esters. The committee graded the evidence for diagnostic utility of each test for the screened conditions. Results: Ample data and experience were available to make strong recommendations for the practice of analyzing amino acids, organic acids, and acylcarnitines. Likewise, strong recommendations were made for the follow-up test menu for many disorders, particularly those with highest prevalence. Fewer data exist to determine the impact of newborn screening on patient outcomes in all but a few disorders. The guidelines also provide an assessment of developing technology that will fuel a refinement of current practice and ultimate expansion of the diseases detectable by tandem mass spectrometry. Conclusions: Guidelines are provided for optimal follow-up testing for positive newborn screens using tandem mass spectrometry. The committee regards these tests as reliable and currently optimal for follow-up testing. .

scholarly journals The Copper(II) Ions Solvent Extraction with a New Compound: 2,6-Bis(4-Methoxybenzoyl)-Diaminopyridine

Processes ◽  
2019 ◽  
Vol 7 (12) ◽  
pp. 954 ◽  
Author(s):  
Daria Bożejewicz ◽  
Katarzyna Witt ◽  
Małgorzata A. Kaczorowska ◽  
Borys Ośmiałowski
Keyword(s):  
Mass Spectrometry ◽  
Solvent Extraction ◽  
High Resolution ◽  
Stability Constant ◽  
Tandem Mass Spectrometry ◽  
High Resolution Mass Spectrometry ◽  
Chloroform Solution ◽  
Tandem Mass ◽  
The Stability ◽  
Resolution Mass

A new compound 2,6-bis(4-methoxybenzoyl)-diaminopyridine (L) was used as an extractant for copper(II) ion recovery in a solvent extraction conducted at a temperature of 25 °C. The best results (99% recovery of copper(II) ions) were obtained when the aqueous phase contained 0.001 mol/dm3 Cu(II) and 0.2 mol/dm3 NH3 (pH~5.8), while the organic phase was a 0.001 mol/dm3 chloroform solution of 2,6-bis(4-methoxybenzoyl)-diaminopyridine. Spectrophotometry studies were used to determine the dissociation constant of the tested compound and determine the stability constant of the complex of subjected compound with copper(II) ions. The high-resolution mass spectrometry (HRMS) and higher energy collisional dissociation tandem mass spectrometry (HCD MS/MS) methods have been applied for the confirmation of the structure of 2,6-bis(4-methoxybenzoyl)-diaminopyridine and to determine its complexation with Cu(II) in solution.

scholarly journals Lanostane-Type Saponins from Vitaliana primuliflora

Molecules ◽  
2019 ◽  
Vol 24 (8) ◽  
pp. 1606 ◽  
Author(s):  
Włodarczyk ◽  
Szumny ◽  
Gleńsk
Keyword(s):  
Mass Spectrometry ◽  
High Resolution Mass Spectrometry ◽  
2D Nmr ◽  
Resonance Spectroscopy ◽  
Tandem Mass ◽  
Triterpenoid Saponins ◽  
The Family ◽  
Chemotaxonomic Markers ◽  
First Time

The phytochemistry of the genera Androsace, Cortusa, Soldanella, and Vitaliana, belonging to the Primulaceae family is not well studied so far. Hence, in this paper, we present the results of UHPLC-MS/MS analysis of several primrose family members as well as isolation and structure determination of two new saponins from Vitaliana primuliflora subsp. praetutiana. These two nor-triterpenoid saponins were characterized as (23S)-17α,23-epoxy-29-hydroxy-3β-[(O-β-d-glucopyranosyl-(1→2)-O-α-l-rhamnopyranosyl-(1→2)-O-β-d-glucopyranosyl-(1→2)-O-α-l-arabinopyranosyl-(1→6)-β-d-glucopyranosyl)oxy]-27-nor-lanost-8-en-25-one and (23S)-17α,23-epoxy-29-hydroxy-3β-[(O-α-l-rhamnopyranosyl-(1→2)-O-β-d-glucopyranosyl-(1→2)-O-α-l-arabinopyranosyl-(1→6)-β-d-glucopyranosyl)oxy]-27-nor-lanost-8-en-25-one, respectively. Their structures were determined by high resolution mass spectrometry (HRMS), tandem mass spectrometry (MS/MS), one- and two-dimensional nuclear magnetic resonance spectroscopy (1D-, and 2D-NMR) analyses. So far, the 27-nor-lanostane monodesmosides were rarely found in dicotyledon plants. Therefore their presence in Vitaliana and also in Androsace species belonging to the Aretia section is unique and reported here for the first time. Additionally, eleven other saponins were determined by HRMS and MS/MS spectra. The isolated lanostane saponins can be considered as chemotaxonomic markers of the family Primulaceae.

scholarly journals Development and validation of sensitive method for determination of serum cotinine in smokers and nonsmokers by liquid chromatography/atmospheric pressure ionization tandem mass spectrometry

1997 ◽  
Vol 43 (12) ◽  
pp. 2281-2291 ◽  
Author(s):  
John T Bernert ◽  
Wayman E Turner ◽  
James L Pirkle ◽  
Connie S Sosnoff ◽  
James R Akins ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Atmospheric Pressure ◽  
High Resolution Mass Spectrometry ◽  
Limit Of Detection ◽  
Atmospheric Pressure Chemical Ionization ◽  
Current Method ◽  
Specific Method ◽  
Tandem Mass ◽  
Serum Samples ◽  
Serum Cotinine

Abstract We describe a sensitive and specific method for measuring cotinine in serum by HPLC coupled to an atmospheric pressure chemical ionization tandem mass spectrometer. This method can analyze 100 samples/day on a routine basis, and its limit of detection of 50 ng/L makes it applicable to the analysis of samples from nonsmokers potentially exposed to environmental tobacco smoke. Analytical accuracy has been demonstrated from the analysis of NIST cotinine standards and from comparative analyses by both the current method and gas chromatography/high-resolution mass spectrometry. Precision has been examined through the repetitive analysis of a series of bench and blind QC materials. This method has been applied to the analysis of cotinine in serum samples collected as part of the Third National Health and Nutrition Examination Survey (NHANES III).

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