Significantly altered metabolites were imported into Mass Profiler Professional (MPP, Version 15.0) ID Browser (version 10.0). Tentative metabolite IDs (25 (link)) were assigned using the Agilent MassHunter METLIN Metabolomics Database (curated in Agilent PCDL Manager, version B.08.00). Compounds were annotated in the first instance by Library/Database search, and by formula generation when there were no Library/Database hits. LC/MS tolerances for precursor ion m/z were ± 10ppm + 2mDa. Identification parameter (Database search, Molecular Formula Generation score) score weights were all evenly set to 40. Search results were limited to the 10 best hits per compound and scores above 70 were considered reliable. Features were annotated with tentative metabolite IDs assigned based on 1) score, 2) the presence of a commercialised standard, and 3) brief literature review to determine likelihood of metabolite’s impact on human monocyte function. Endogenous metabolites (as listed in HMDB) were preferred. Where no metabolite IDs or formulae were available, metabolite features were annotated by their mass and RT values (e.g., 601.2048@4.95).
Pcdl manager
Manufactured by Agilent Technologies
Sourced in United States
PCDL Manager is a software tool provided by Agilent Technologies that allows users to create, manage, and apply Personal Compound Database Libraries (PCDLs) for use with Agilent mass spectrometry systems. The core function of PCDL Manager is to facilitate the organization and utilization of custom compound libraries within Agilent's analytical workflows.
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6 protocols using pcdl manager
1
Metabolomic Profiling of Monocyte Function
2
Analyzing Tobacco Additive Composition
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MassHunter Software of Qualitative Analysis version B.07.00 (Agilent Technologies), Quantitative Analysis for TOF version B.07.01 (Agilent Technologies), and PCDL Manager version B.07.00 (Agilent Technologies) were used for data analysis. Mass spectra were compared with the NIST mass spectral library version 2.0 2011 (NIST, Gaithersburg, MD). The general flavour description of the compounds and information on their use as tobacco additives was extracted from the Leffingwell Flavor-Base (10th edition, Leffingwell & Associates, Canton, GA, USA). Multivariate data analysis was carried out by using SIMCA version 15.0.2. (MKS Umetrics, Malmo, Sweden).
3
Multiomics Data Analysis Pipeline
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The generated raw data was processed by PNNL PreProcessor 3.0 (Version 24 November 2020.) for demultiplexing and chromatographic smoothing. IM-MS Browser (Version 10.0), Mass Profiler (Version 10.0), and PCDL Manager (Version 8.00), all from Agilent Technologies (Waldbronn, Germany), with an in-house library, were used for feature extraction and feature annotation. Statistical analysis was carried out employing the web-based platform of MetaboAnalyst (McGill University, Montreal, QC, Canada). The visualization of the boxplots was completed with OriginPro 2021 (Northampton, MA, USA).
4
Comprehensive Phytochemical Profiling of HBP
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The HBP extract was qualitatively analyzed using ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS) (Agilent 1290–6545, Agilent Technologies, USA). The column used in the method was poroshell 120 column (2.1 × 100 mm, 2.7 μm, Agilent Technology, USA). The column temperature was set to 45°C. The mobile phase consisted of formic acid in water (0.1%) as solvent A and methanol as solvent B using gradient elution. The injection volume of the prepared sample was 2 μL and the flow rate was 0.3 mL/min. The solvent gradient was 0 to 1.5 min, 5% B; 5 min, 15% B; 9 min, 25% B; 16 min, 40% B; 22 min, 55% B; 28 to 30 min, 95% B; and 31 min, 5% B. Mass spectrometry was performed using electrospray source in negative ion mode with full scan, auto MS/MS mode. The capillary voltage was 3,500 V, nozzle voltage was 500 V, drying-gas temperature was 260°C, and sheath gas temperature was 360°C. Mass spectrometry data were analyzed with the MassHunter Workstation Software (Quantitative Analysis B.07.00, PCDL Manager B.07.00, and Molecular Structure Correlator, Agilent Technology, USA).
5
Varietal Fingerprinting of Wines
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Data files were then assessed using MassHunter Mass Profiler and the IM Browser Software (B08.00). Data files were evaluated in batches according to wine type in a non-targeted workflow. For the molecular feature finding step, the common organic molecules isotope model was used, the charge state was limited to between ±1 and ± 2, a minimum extraction threshold of 50 counts (spectral abundance) set, and molecular features were restricted to retention times between 2 and 20 min. Intersample molecular feature alignment used retention time matching of ±0.20 min, and accurate m/z of 10 ppm ± 2 mDa. To enable varietal group fingerprinting, resultant molecular feature lists were further filtered by frequency within a given variety (i.e. presence in !2 samples within the variety). These lists were further refined by Q-Score (!70) and a minimum cut-off abundance of 5000 (average of the monoisotopic ion peak volume). DT CCS N2 values of the authentic standards measured using an established standardized method [24] (link) were added to a compound library for supporting identification confirmation via Agilent PCDL Manager (B.08.00).
6
Suspect Screening Method for Dental Products
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For suspect screening on LC-QTOF-MS/MS, an in-house library using the Personal Compound Database and Library (PCDL) Manager (Version Rev. B.07.01, Agilent Technologies, Santa Clara, USA) was prepared to facilitate the identification of chromatographic peaks. Based on literature, compounds were included when previously identified in leaching experiments (7, 19, 22, 36) . Secondly, materials safety data sheets of dental products were screened and stated components were included in the database. The molecular formula and mono-isotopic mass were added to the database for all compounds. For compounds where an analytical standard was available, retention time and MS/MS spectra were also added to the database after analysis on the LC-QTOF-MS system.
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