scholarly journals A Data-Challenge Case Study of Analyte Detection and Identification with Comprehensive Two-Dimensional Gas Chromatography with Mass Spectrometry (GC×GC-MS)

Separations ◽  
2019 ◽  
Vol 6 (3) ◽  
pp. 38
Author(s):  
Stephen E. Reichenbach ◽  
Qingping Tao ◽  
Chiara Cordero ◽  
Carlo Bicchi
Keyword(s):  
Mass Spectrometry ◽  
New Method ◽  
Two Dimensional ◽  
Spectral Library ◽  
Mass Spectral ◽  
Detection And Identification ◽  
Percent Response ◽  
Analyte Detection ◽  
Detector Saturation

This case study describes data analysis of a chromatogram distributed for the 2019 GC×GC Data Challenge for the Tenth Multidimensional Chromatography Workshop (Liege, Belgium). The chromatogram resulted from chemical analysis of a terpene-standards sample by comprehensive two-dimensional chromatography with mass spectrometry (GC×GC-MS). First, several aspects of the data quality are assessed, including detector saturation and oscillation, and operations to prepare the data for analyte detection and identification are described, including phase roll for modulation-cycle alignment and baseline correction to account for the non-zero detector baseline. Then, the case study presents operations for analyte detection with filtering, a new method to flag false detections, interactive review to confirm detected peaks, and ion-peaks detection to reveal peaks that are obscured by noise or coelution. Finally, the case study describes analyte identification including mass-spectral library search with a new method for optimizing spectra extraction, retention-index calibration from preliminary identifications, and expression-based identification checks. Processing of the first 40 min of data detected 144 analytes, 21 of which have at least one percent response, plus an additional 20 trace and/or coeluted analytes.

scholarly journals N-Linked Glycopeptide Identification Based on Open Mass Spectral Library Search

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Zhiwu An ◽  
Qingbo Shu ◽  
Hao Lv ◽  
Lian Shu ◽  
Jifeng Wang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Human Cancer ◽  
Cancer Cell Line ◽  
Peptide Identification ◽  
High Energy ◽  
Mass Spectral Library ◽  
Spectral Library ◽  
Data Set ◽  
Library Search ◽  
Mass Spectral

Confident characterization of intact glycopeptides is a challenging task in mass spectrometry-based glycoproteomics due to microheterogeneity of glycosylation, complexity of glycans, and insufficient fragmentation of peptide bones. Open mass spectral library search is a promising computational approach to peptide identification, but its potential in the identification of glycopeptides has not been fully explored. Here we present pMatchGlyco, a new spectral library search tool for intact N-linked glycopeptide identification using high-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS) data. In pMatchGlyco, (1) MS/MS spectra of deglycopeptides are used to create spectral library, (2) MS/MS spectra of glycopeptides are matched to the spectra in library in an open (precursor tolerant) manner and the glycans are inferred, and (3) a false discovery rate is estimated for top-scored matches above a threshold. The efficiency and reliability of pMatchGlyco were demonstrated on a data set of mixture sample of six standard glycoproteins and a complex glycoprotein data set generated from human cancer cell line OVCAR3.

scholarly journals Identification of Leishmania by Matrix-Assisted Laser Desorption Ionization–Time of Flight (MALDI-TOF) Mass Spectrometry Using a Free Web-Based Application and a Dedicated Mass-Spectral Library

2017 ◽  
Vol 55 (10) ◽  
pp. 2924-2933 ◽  
Author(s):  
Laurence Lachaud ◽  
Anna Fernández-Arévalo ◽  
Anne-Cécile Normand ◽  
Patrick Lami ◽  
Cécile Nabet ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Leishmania Donovani ◽  
Identification System ◽  
Enzyme Electrophoresis ◽  
Mass Spectral Library ◽  
Spectral Library ◽  
Web Based ◽  
Content Type ◽  
Mass Spectral ◽  
Scalable Database

ABSTRACT Human leishmaniases are widespread diseases with different clinical forms caused by about 20 species within the Leishmania genus. Leishmania species identification is relevant for therapeutic management and prognosis, especially for cutaneous and mucocutaneous forms. Several methods are available to identify Leishmania species from culture, but they have not been standardized for the majority of the currently described species, with the exception of multilocus enzyme electrophoresis. Moreover, these techniques are expensive, time-consuming, and not available in all laboratories. Within the last decade, mass spectrometry (MS) has been adapted for the identification of microorganisms, including Leishmania . However, no commercial reference mass-spectral database is available. In this study, a reference mass-spectral library (MSL) for Leishmania isolates, accessible through a free Web-based application (mass-spectral identification [MSI]), was constructed and tested. It includes mass-spectral data for 33 different Leishmania species, including species that infect humans, animals, and phlebotomine vectors. Four laboratories on two continents evaluated the performance of MSI using 268 samples, 231 of which were Leishmania strains. All Leishmania strains, but one, were correctly identified at least to the complex level. A risk of species misidentification within the Leishmania donovani , L. guyanensis , and L. braziliensis complexes was observed, as previously reported for other techniques. The tested application was reliable, with identification results being comparable to those obtained with reference methods but with a more favorable cost-efficiency ratio. This free online identification system relies on a scalable database and can be implemented directly in users' computers.

scholarly journals Curatr: a web application for creating, curating, and sharing a mass spectral library

2017 ◽  
Author(s):  
Andrew Palmer ◽  
Prasad Phapale ◽  
Dominik Fay ◽  
Theodore Alexandrov
Keyword(s):  
Mass Spectrometry ◽  
Web Application ◽  
Mass Spectrometry Analysis ◽  
Supplementary Information ◽  
Spectral Library ◽  
Mass Spectral Fragmentation ◽  
Mass Spectral ◽  
Link Type ◽  
Manual Curation

AbstractMotivationIdentification from metabolomics mass spectrometry experiments requires comparison of fragmentation spectra from experimental samples to spectra from analytical standards. As the quality of identification depends directly on the quality of the reference spectra, manual curation is routine during the selection of reference spectra to include in a spectral library. Whilst building our own in-house spectral library we realised that there is currently no vendor neutral open access tool for for facilitating manual curation of spectra from raw LC-MS data into a custom spectral library.ResultsWe developed a web application curatr for the rapid generation of high quality mass spectral fragmentation libraries for liquid-chromatography mass spectrometry analysis. Curatr handles datasets from single or multiplexed standards, automatically extracting chromatographic profiles and potential fragmentation spectra for multiple adducts. These are presented through an intuitive interface for manual curation before being documented in a custom spectral library. Searchable molecular information and the providence of each standard is stored along with metadata on the experimental protocol. Curatr support the export of spectral libraries in several standard formats for easy use with third party software or submission to community databases, maximising the return on investment for these costly measurements. We demonstrate the use of curatr to generate the EMBL Metabolomics Core Facility spectral library which is publicly available at http://curatr.mcf.embl.de.AvailabilityThe source code is freely available at http://github.com/alexandrovteam/curatr/ along with example data.Supplementary informationA step-by step user manual is available in the supplementary information

scholarly journals Climate and Processing Effects on Tea (Camellia sinensis L. Kuntze) Metabolome: Accurate Profiling and Fingerprinting by Comprehensive Two-Dimensional Gas Chromatography/Time-of-Flight Mass Spectrometry

Molecules ◽  
2020 ◽  
Vol 25 (10) ◽  
pp. 2447 ◽  
Author(s):  
Federico Stilo ◽  
Giulia Tredici ◽  
Carlo Bicchi ◽  
Albert Robbat ◽  
Joshua Morimoto ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Gas Chromatography ◽  
South Carolina ◽  
Antioxidant Properties ◽  
Time Of Flight ◽  
Black Tea ◽  
Two Dimensional ◽  
Mass Spectral ◽  
Flight Mass Spectrometry ◽  
Analytical Approaches

This study applied an untargeted–targeted (UT) fingerprinting approach, based on comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-TOF MS), to assess the effects of rainfall and temperature (both seasonal and elevational) on the tea metabolome. By this strategy, the same compound found in multiple samples need only to be identified once, since chromatograms and mass spectral features are aligned in the data analysis process. Primary and specialized metabolites of leaves from two Chinese provinces, Yunnan (pu′erh) and Fujian (oolong), and a farm in South Carolina (USA, black tea) were studied. UT fingerprinting provided insight into plant metabolism activation/inhibition, taste and trigeminal sensations, and antioxidant properties, not easily attained by other analytical approaches. For example, pu′erh and oolong contained higher relative amounts of amino acids, organic acids, and sugars. Conversely, black tea contained less of all targeted compounds except fructose and glucose, which were more similar to oolong tea. Findings revealed compounds statistically different between spring (pre-monsoon) and summer (monsoon) in pu′erh and oolong teas as well as compounds that exhibited the greatest variability due to seasonal and elevational differences. The UT fingerprinting approach offered unique insights into how differences in growing conditions and commercial processing affect the nutritional benefits and sensory characteristics of tea beverages.

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