Fitting Structure-Data Files (.SDF) Libraries to Progenesis QI Identification Searches

Sanches, Pedro Henrique Godoy; Oliveira, Danilo de; Reis, Ivan Gustavo Masselli dos; Fernandes, Anna Maria A. P.; Silva, Alex; Eberlin, Marcos N.; Carvalho, Patrícia de Oliveira; Duarte, Gustavo; Porcari, Andréia M.

doi:10.21577/0103-5053.20230016

Cited by 4 publications

(2 citation statements)

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“…Fragmentation profile, mass accuracy, mass error, and isotope similarity were evaluated to accept the annotated molecules. To allow the compatibility of Progenesis PQI data and external SDF-based spectra libraries, we used an in-house software named “SDF2PQI” to increase the number of fragment matches [ 28 ]. SDF2PQI was recently detailed elsewhere and is available free of charge.…”

Section: Methodsmentioning

confidence: 99%

Glycerophospholipids in Red Blood Cells Are Associated with Aerobic Performance in Young Swimmers

Silva,

Bertolucci,

Scariot

et al. 2024

Nutrients

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This study aimed to characterize the composition of lipids in the red blood cells (RBCs) of adolescent swimmers and correlate this lipidome with the aerobic performance of the athletes. Five experimental assessments were performed by 37 adolescent swimmers. During the first session, the athletes went to the laboratory facility for venous blood sampling. The critical velocity protocol was conducted over the 4 subsequent days to measure aerobic performance (CV), comprising maximal efforts over distances of 100, 200, 400, and 800 m in a swimming pool. RBCs were obtained and extracted for analysis using the liquid chromatography—high resolution mass spectrometry untargeted approach. A total of 2146 ions were detected in the RBCs, of which 119 were identified. The enrichment pathway analysis indicated intermediary lipids in the glycerophospholipid, glycerolipid, sphingolipid, linoleic acid, and alpha-linolenic metabolisms, as well as pentose and glucuronate interconversions. A significant impact of the intermediary lipids was observed for the glycerophospholipid metabolism, including phosphatidylethanolamine (PE), phosphatidylcholine (PC), 1-acyl-sn-glycero-3-phosphocholine, sn-glycerol 3-phosphate, and phosphatidic acid. Inverse and significant associations were observed for PE 18:2/18:3 (r = −0.39; p = 0.015), PC 18:3/20:0 (r = −0.33; p = 0.041), and phosphatidic acid 18:0/0:0 (r = −0.47; p = 0.003) with aerobic performance. Swimmers who exhibited higher levels of aerobic performance also had the lowest abundance of PE, PC, and phosphatidic acid.

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Section: Methodsmentioning

confidence: 99%

Glycerophospholipids in Red Blood Cells Are Associated with Aerobic Performance in Young Swimmers

Silva,

Bertolucci,

Scariot

et al. 2024

Nutrients

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“…For each mass spectrometer, the scanning frequency was 0.2 s. Peak extraction and alignment were performed using Progenesis QI software (v3.0) with raw data collected by MassLynx v4.2. Peak identification was based on the online METLIN database attached to the Progenesis QI software (v3.0) and BioMarker’s self-built database [ 28 ]. In a mass spectrometry (MS) system, molecular cleavage patterns follow certain rules and contain valuable information about the chemical structures.…”

Section: Methodsmentioning

confidence: 99%

Longitudinal Distribution Map of the Active Components and Endophytic Fungi in Angelica sinensis (Oliv.) Diels Root and Their Potential Correlations

Sun,

Guo,

Geng

et al. 2024

Metabolites

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The three distinct medicinal parts of Angelica sinensis (Oliv.) Diels (Ang) roots are the head, body, and tail (ARH, ARB, and ART, respectively). How endophytic fungi shape the differences in metabolic components among these parts remains unclear. We quantified the distribution of active components and endophytic fungi along the ARH, ARB, and ART and their relationships. Based on the metabolic components and their abundances detected via non-target metabolism, the different medicinal parts were distinguishable. The largest number of dominant metabolic components was present in ART. The difference between ART and ARH was the greatest, and ARB was in a transitional state. The dominant active molecules in ART highlight their effects in haemodynamics improvement, antibacterial, anti-inflammatory, and hormone regulation, while ARH and ARB indicated more haemostasis, blood enrichment, neuromodulation, neuroprotection and tranquilisation, hepatoprotection, and antitumour activities than that of ART. The ARHs, ARBs, and ARTs can also be distinguished from each other based on the endophytic fungi at the microbiome level. The most dominant endophytic fungi were distributed in ART; the differences between ART and ARH were the largest, and ARB was in a transition state, which is consistent with the metabolite distributions. Structural equation modelling showed that the endophytic fungi were highly indicative of the metabolic components. Correlation analysis further identified the endophytic fungi significantly positively correlated with important active components, including Condenascus tortuosus, Sodiomyces alcalophilus, and Pleotrichocladium opacum. The bidirectional multivariate interactions between endophytic fungi and the metabolic components shape their spatial variations along the longitudinal direction in the Ang root.

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A Platform for the Study of Drug Interactions and Adverse Effects Prediction

Mendes

Camacho

2023

Bioinformatics and Biomedical Engineering

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Fitting Structure-Data Files (.SDF) Libraries to Progenesis QI Identification Searches

Cited by 4 publications

References 0 publications

Glycerophospholipids in Red Blood Cells Are Associated with Aerobic Performance in Young Swimmers

Glycerophospholipids in Red Blood Cells Are Associated with Aerobic Performance in Young Swimmers

Longitudinal Distribution Map of the Active Components and Endophytic Fungi in Angelica sinensis (Oliv.) Diels Root and Their Potential Correlations

A Platform for the Study of Drug Interactions and Adverse Effects Prediction

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