Comparing Targeted vs. Untargeted MS2 Data-Dependent Acquisition for Peak Annotation in LC–MS Metabolomics

Ten-Doménech, Isabel; Martínez-Sena, Teresa; Moreno-Torres, Marta; Sanjuan-Herráez, Juan Daniel; Castell, José V.; Parra-Llorca, Anna; Vento, Máximo; Quintás, Guillermo; Kuligowski, Julia

doi:10.3390/metabo10040126

Cited by 32 publications

(25 citation statements)

References 16 publications

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“…Automatic metabolite annotation was carried out as described elsewhere using the following parameters: spectral libraries: HMDB () and LipidBlast; m / z accuracy in both precursor and fragment ions (5 mDa); weight of m / z and intensity for the calculation of the dot product and reverse dot product (in this study, m = 1.2 and n = 0.9 for dp and rdp , respectively); minimum number of matching ions in the experimental and reference spectra: 3; absolute and relative intensity thresholds in the MSMS spectra: 0.01% of the base peak and 200 AU; and minimum mean dot product : 0.75. Metabolite annotation using LipidBlast was carried out using LipiDex using 0.01 Da tolerances in both MS (precursor) and MS 2 (fragment) data …”

Section: Materials and Methodsmentioning

confidence: 99%

Toward Rapid Screening of Liver Grafts at the Operating Room Using Mid-infrared Spectroscopy

Pérez-Guaita

Moreno-Torres²,

Jover

et al. 2020

Anal. Chem.

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The estimation of steatosis in a liver graft is mandatory prior to liver transplantation, as the risk of graft failure increases with the level of infiltrated fat. However, the assessment of liver steatosis before transplantation is typically based on a qualitative or semiquantitative characterization by visual inspection and palpation and histological analysis. Thus, there is an unmet need for transplantation surgeons to have access to a diagnostic tool enabling an in situ fast classification of grafts prior to extraction. In this study, we have assessed an attenuated total reflection–Fourier transform infrared (ATR–FTIR) spectroscopic method compatible with the requirements of an operation room for the evaluation of the lipid contents in human livers. A set of 20 human liver biopsies obtained from organs intended for transplantation were analyzed by expert pathologists, ATR–FTIR spectroscopy, lipid biochemical analysis, and UPLC–ESI(+/−)TOFMS for lipidomic profiling. Comparative analysis of multisource data showed strong correlations between ATR–FTIR, clinical, and lipidomic information. Results show that ATR–FTIR captures a global picture of the lipid composition of the liver, along with information for the quantification of the triradylglycerol content in liver biopsies. Although the methodology performance needs to be further validated, results support the applicability of ATR–FTIR for the in situ determination of the grade of liver steatosis at the operation room as a fast, quantitative method, as an alternative to the qualitative and subjective pathological examination.

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Section: Materials and Methodsmentioning

confidence: 99%

Toward Rapid Screening of Liver Grafts at the Operating Room Using Mid-infrared Spectroscopy

Pérez-Guaita

Moreno-Torres²,

Jover

et al. 2020

Anal. Chem.

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“…LC–MS features were also excluded if the maximum peak area value in blanks multiplied by 10 was larger than the median value in samples, and those annotated as drug metabolites or food components. Metabolite annotation was carried out based on MS/MS data using the Human Metabolome Database ( http://www.hmdb.ca ) and METLIN ( http://www.metlin.scripps.edu ) databases, and LipiDex (Hutchins et al 2018 ) as described elsewhere (Ten-Doménech et al 2020 ) with 0.015 Da or 20 ppm accuracy. Information regarding classes and subclasses of the metabolites was downloaded from the HMDB ( http://www.hmdb.ca ) and automatically incorporated to the annotation.…”

Section: Methodsmentioning

confidence: 99%

Metabolomic analysis to discriminate drug-induced liver injury (DILI) phenotypes

Quintás

Martínez-Sena²,

Conde

et al. 2021

Arch Toxicol

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Drug-induced liver injury (DILI) is an adverse toxic hepatic clinical reaction associated to the administration of a drug that can occur both at early clinical stages of drug development, as well after normal clinical usage of approved drugs. Because of its unpredictability and clinical relevance, it is of medical concern. Three DILI phenotypes (hepatocellular, cholestatic, and mixed) are currently recognized, based on serum alanine aminotransferase (ALT) and alkaline phosphatase (ALP) values. However, this classification lacks accuracy to distinguish among the many intermediate mixed types, or even to estimate the magnitude and progression of the injury. It was found desirable to have additional elements for better evaluation criteria of DILI. With this aim, we have examined the serum metabolomic changes occurring in 79 DILI patients recruited and monitored using established clinical criteria, along the course of the disease and until recovery. Results revealed that free and conjugated bile acids, and glycerophospholipids were among the most relevant metabolite classes for DILI phenotype characterization. Using an ensemble of PLS–DA models, metabolomic information was integrated into a ternary diagram to display the disease phenotype, the severity of the liver damage, and its progression. The modeling implemented and the use of such compiled information in an easily understandable and visual manner facilitates a straightforward DILI phenotyping and allow to monitor its progression and recovery prediction, usefully complementing the concise information drawn out by the ALT and ALP classification.

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“…Parameters employed for HM fingerprinting have been described elsewhere [30]. In summary, OMM and DHM samples were subjected to a single-phase extraction procedure by adding 175 mL of CH 3 OH followed by 175 mL of MTBE [31] and 20 mL of supernatant were added to 80 mL of a CH 3 OH:MTBE (1:1, v/v) solution.…”

Section: Hm Preparation and Analysismentioning

confidence: 99%

“…The pre-processing pipeline for data acquired during the analysis of HM samples has been described elsewhere [30]. For urine, centroid LC-QTOFMS raw data were converted to mzXML format employing ProteoWizard [34] (http://proteowizard.sourceforge.…”

Section: Data Processing and Statistics 241 Metabolomics Data Pre-processingmentioning

confidence: 99%

Effect of donor human milk on host-gut microbiota and metabolic interactions in preterm infants

et al. 2021

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Background & aims: Human milk is the gold standard for infant nutrition. Preterm infants whose mothers are unable to provide sufficient own mother's milk (OMM), receive pasteurized donor human milk (DHM). We studied metabolic signatures of OMM and DHM and their effect on the interplay of the developing microbiota and infant's metabolism. Methods: Metabolic fingerprinting of OMM and DHM as well as infant's urine was performed using liquid chromatographyemass spectrometry and the infant's stool microbiota was analyzed by 16S rRNA sequencing. Results: Significant differences in the galactose and starch and sucrose metabolism pathways when comparing OMM and DHM, and alterations of the steroid hormone synthesis and pyrimidine metabolism pathways in urine were observed depending on the type of feeding. Differences in the gut-microbiota composition were also identified. Conclusion:The composition of DHM differs from OMM and feeding of DHM has a significant impact on the metabolic phenotype and microbiota of preterm infants. Our data help to understand the origin of the observed changes generating new hypothesis: i) steroid hormones present in HM have a significant influence in the activity of the steroid hormone biosynthesis pathway in preterm infants; ii) the pyrimidine metabolism is modulated in preterm infants by the activity of gut-microbiota. Short-and longterm implications of the observed changes for preterm infants need to be assessed in further studies.

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Comparing Targeted vs. Untargeted MS2 Data-Dependent Acquisition for Peak Annotation in LC–MS Metabolomics

Cited by 32 publications

References 16 publications

Toward Rapid Screening of Liver Grafts at the Operating Room Using Mid-infrared Spectroscopy

Toward Rapid Screening of Liver Grafts at the Operating Room Using Mid-infrared Spectroscopy

Metabolomic analysis to discriminate drug-induced liver injury (DILI) phenotypes

Effect of donor human milk on host-gut microbiota and metabolic interactions in preterm infants

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