Total Ion Chromatograms (TIC) obtained with the GC-MS were visually examined. After chromatogram inspection, the software Agilent MassHunter Unknowns Analysis (B.09.00, Agilent Technologies) was used to perform a deconvolution of the signals. Further, Agilent Mass Profiler Professional software (version 13.0, Agilent Technologies) was used for signal alignment. After obtaining the list of compounds, NIST 14 (National Institute of Standards and Technology Mass Spectral Library v.2.2, 2014) and Fiehn RTL library (version 2013) [23] were used for metabolite identification comparing their mass fragmentation patterns [15] . Due to the quality assurance procedure, only metabolites present in more than 75% of samples and with CV less than 20% were kept. Data was normalized according to the internal standard, 20 ppm tricosane in heptane.
Agilent mass profiler professional
Manufactured by Agilent Technologies
Sourced in United States
Agilent Mass Profiler Professional is a data analysis software that enables the processing and statistical analysis of mass spectrometry data. It provides tools for peak detection, alignment, and normalization of data from various mass spectrometry platforms.
Automatically generated - may contain errors
Lab products found in correlation
Agilent masshunter unknowns analysis, by Agilent Technologies (2 mentions)
Qiaamp powerfecal pro dna kit, by Qiagen (1 mentions)
Masshunter profinder, by Agilent Technologies (1 mentions)
Masshunter workstation qualitative software, by Agilent Technologies (1 mentions)
Metlin metabolomics database, by Agilent Technologies (1 mentions)
Agilent masshunter quantitative analysis, by Agilent Technologies (1 mentions)
4 protocols using agilent mass profiler professional
1
GC-MS Metabolite Identification Pipeline
2
Cecal Microbiome Sampling Protocol
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Cecal luminal feces were collected from 48 birds, with 4 birds from each treatment at the ages of 14, 21, and 28 d. The collected samples were promptly frozen in liquid nitrogen and stored at -80°C until further analysis. Genomic DNA was extracted from the samples using the QIAamp PowerFecal Pro DNA kit (QIAGEN, Hilden, Germany), following the manufacturer's instructions. Subsequently, DNA quantification and quality assessment were carried out using Agilent Mass Profiler Professional (Agilent Technologies, Santa Clara, CA).
3
Untargeted Metabolomics Profiling Workflow
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A matrix of molecular features characterized by mass to charge ratio (m/z) and retention time (RT) was generated using Agilent MassHunter Workstation Qualitative software version B07.00, Agilent MassHunter Profinder (version B.08.00), Agilent Mass Profiler Professional (MPP version 14.5) and Agilent Personal Compound Database Library (PCDL) (Agilent Technologies, Santa Clara, CA, USA). The parameters for molecular extracts and peak binning/alignment using Profinder were as follows; peak height ≥ 10,000 counts, compound ion count threshold two or more ions, compound alignment tolerances were 0.00% + 0.15 minutes for RT and 20.00 ppm + 2.00 mDa for mass. The extracted ion chromatogram was smoothed with Gaussian smoothing before integration. The data files were converted to compound exchange files (.cef) format and visualized and analyzed in MPP using multivariate analysis including principal component analysis. Features present in a minimum of three out of five replicates were included for further analysis. Identification was performed comparing the generated database to the METLIN metabolomics database (version B 07.00, Agilent Technologies, Santa Clara, CA, USA) and confirmed using available standards based on accurate mass, retention time (RT) and mass spectra.
4
Data Processing of Multiomics Analyses
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Liquid chromatography–mass spectrometry and CE–MS data processing were performed in MassHunter Profinder software version B.06.00 using Molecular Feature Extraction and Recursive Feature Extraction tools. For GC–MS data treatment, deconvolution and identification were carried out using Agilent MassHunter Unknowns Analysis version B.07.00. Data obtained in the Unknowns Analysis Tool were aligned in Agilent Mass Profiler Professional version B.12.1 and exported to Agilent MassHunter Quantitative Analysis version B.07.00 to obtain the abundance of the compounds. Data matrix obtained from Profinder (CE–MS and LC–MS data) and Quantitative analysis (GC–MS data) were exported to Excel Software (Microsoft Office 2013) for data filtration. As the QC surrogate was used, features were filtered by selecting the data present in at least 80% of the samples in 1 of the 2 groups: cachexia and controls (Appendix S1 ).
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