All data was collected using MassLynx4.1 (Waters, Manchester, UK) and processing was performed in UNIFI 1.9 (Waters, Manchester, UK). The components were identified in a nontargeted manner by spectral deconvolution in UNIFI 1.9 (Waters, Manchester, UK) by the following 3D peak detection features; low-energy limits of 150 and high-energy limits of 20, isotope clustering, and high-to low energy association within a 0.5 fraction of the chromatographic and drift peak with a mass accuracy of ±2 mDa. The maximum number of allowed fragment ions per match was set at 10.
Unifi 1
Manufactured by Waters Corporation
Sourced in United States, United Kingdom
The UNIFI 1.8 is a high-performance liquid chromatography (HPLC) system designed for analytical and preparative applications. It features a compact, modular design and is capable of delivering precise and consistent results. The UNIFI 1.8 is equipped with advanced software and hardware components to ensure reliable and efficient operation.
Automatically generated - may contain errors
Lab products found in correlation
Acquity uplc 1 class, by Waters Corporation (5 mentions)
Hipersolv, by Avantor (5 mentions)
Masslynx v4, by Waters Corporation (5 mentions)
Masslynx 4, by Waters Corporation (4 mentions)
Acquity c 18 uplc column, by Waters Corporation (4 mentions)
Acquity uplc beh c18 column, by Waters Corporation (3 mentions)
Vion ims qtof, by Waters Corporation (3 mentions)
Ezinfo software 3, by Sartorius (3 mentions)
Xevo g2 s qtof mass spectrometer, by Waters Corporation (2 mentions)
Progenesis qi v2, by Waters Corporation (2 mentions)
Acquity uplc system, by Waters Corporation (2 mentions)
Pngase f, by New England Biolabs (2 mentions)
Progenesis qi 2, by Waters Corporation (1 mentions)
Ezinfo, by Waters Corporation (1 mentions)
Progenesis qi, by Waters Corporation (1 mentions)
Acquity uplc, by Waters Corporation (1 mentions)
Waters acquity uplc system, by Waters Corporation (1 mentions)
C18 column, by Thermo Fisher Scientific (1 mentions)
Markerlynx application manager, by Waters Corporation (1 mentions)
Ezinfo 3, by Waters Corporation (1 mentions)
50 protocols using unifi 1
1
Nontargeted Metabolite Profiling with UNIFI
2
Metabolomics Data Analysis Pipeline
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The profiling data were acquired using UNIFI 1.8 software (Waters, Milford, MA, USA) and processed using Progenesis QI 2.1 software with EZinfo (Waters, Milford, MA, USA). The LC-MS signals acquired in ESI+ and ESI- modes were uploaded to Progenesis QI with EZinfo for data normalization, peak picking, compound measurement, and statistical analysis. The LC-MS signals were then converted to datasets by using Progenesis QI. The datasets were subjected to statistical and pathway analysis by applying the MetaboAnalysis 5.0 tool (https://www.metaboanalyst.ca/MetaboAnalyst/ accessed on 14 September 2022). The level of each metabolite was estimated by the peak area of the chromatogram for each identified metabolite using UNIFI 1.8 software (Waters, Milford, MA, USA).
3
Chrysanthemum coronarium L. Phytochemical Analysis
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The dried CC (1 kg) was crushed and extracted twice with 10 L of 50% ethanol for 24 h. After filtration, the extracts were evaporated by rotary evaporator and freeze-dried at −70 °C. The extraction yield was 8% (w/w). All experiments on Chrysanthemum coronarium L. leaves were performed in accordance with the institutional, national, and international guidelines and legislation. CC (10 mg) was dissolved in 50% MeOH (10 mL), and the chemical profile of the extract was analyzed using UPLC-tunable UV (TUV) (Waters, Milford, MA, USA) with an Acquity UPLC BEH C18 column (100 × 2.1 mm, 1.7 μm; Waters). The eluted compounds were analyzed by Q-TOF/MS (Waters) in the negative electrospray ionization mode under optimized conditions as follows: a scan range of 50–1500 m/z, a scan time of 0.2 s, a capillary voltage of 2.5 kV, a sampling cone voltage of 40 V, a desolvation flow rate of 900 L/h, a desolvation temperature of 400 °C, source temperature of 100 °C, and sample injection volume of 1 μL. MS/MS spectra were acquired under collision energy ramp (10–30 eV). The major compounds were identified based on the online database UNIFI 1.8.2 (Waters) and other online databases, such as ChemSpider, Traditional Chinese Medicine database, and METLIN [16 (link)].
4
Untargeted Metabolomics Data Processing
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Raw data were processed under default parameters as a UNIFI file (UNIFI 1.8.2, Waters Corp., Milford, United States), which was exported to Progenesis QI (version 3.0.7, Waters Corp., Milford, United States). For the alignment, retention times below 0.5 min and after 18 min were excluded. A width peak of 0.06 s was defined. Deconvolution was automatically performed, considering M + H, M + Na, M + H-H20, M + K, and M + NH4 as adducts. However, manual inspection was done, eliminating those features with incorrect alignment in chromatograms and neutral and m/z mass. An excel file was exported and a signal to noise (S/N) ratio was calculated for each sample based on the extraction blank. All features with a S/N < 5 in the 80% of samples were eliminated. Besides, RSD was calculated taking QCs as references. Features with RSD > 20% were also eliminated.
5
UHPLC-HR-MS Dereplication Protocol
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UHPLC-HR-MS data for dereplication was recorded using an Acquity I-class UPLC (Waters, Milford, MA, USA) coupled to a PDA detector and a Vion IMS QToF (Waters). The chromatographic separation was performed using an Acquity C-18 UPLC column (1.7 µm, 2.1 mm × 100 mm) (Waters). Mobile phases consisted out of acetonitrile (HiPerSolv, VWR) for mobile phase A and ddH2O produced by the in-house Milli-Q system as mobile phase B, both containing 1% formic acid (v/v) (33015, Sigma). The gradient was run from 10% to 90% B in 12 min at a flow rate of 0.45 mL/min. Samples were run in ESI+ and ESI- ionization mode. The data was processed and analyzed using UNIFI 1.8.2 (Waters).
6
MS Data Processing and PCA Analysis
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All MSE data were collected and processed using UNIFI 1.8 (Waters Corp., Milford, MA, USA). Data within UNIFI 1.8 is passed through the apex peak detection and alignment processing algorithms. The intensity of each ion was normalized with respect to the total ion count to generate a data matrix having RT, m/z value, and the normalized peak area. Charged species, salt adducts, and fragments are all automatically aligned and grouped. The three-dimensional data including peak number (RT-m/z pair), sample name, and normalized peak areas were exported to the EZinfo software 3.0.3 (UMETRICS, Umea, Sweden) for PCA. The data were mean-centered and Pareto-scaled prior to PCA.
7
Disulfide Bond Mapping of Monoclonal Antibodies
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100 μg of mAb was incubated for 20 minutes at 57 °C in denaturing buffer (6 M guanidine hydrochloride, 50 mM Tris and 5 mM EDTA, pH 8). Each sample was prepared in duplicate; to one replicate 2.5 μL iodoacetamide (300 mM in 200 mM sodium phosphate, pH 6.5) was added and to the other 2.5 μL of water was added. A further 100 μL of water was added to each sample to dilute the guanidine hydrochloride. Lys-C was added in a 1 : 100 ratio and incubated at 37 °C overnight. TFA was added to a final concentration of 1%. Samples were analysed via LC-MS using a Waters Acquity UPLC coupled to a Waters Vion mass spectrometer operated in positive ion/resolution mode. The chromatographic separation was achieved using a Waters Acquity BEH C18 Peptide column (2.1 × 100 mm, 1.7 μm) and an LC gradient supplied at 0.25 ml min–1, over 90 min up to 90% organic (mobile phases; water, acetonitrile and 1% TFA). Waters UNIFI™ 1.8 was used to generate a list of possible disulphide bond linkages.
8
UPLC/QTOF MS Analysis of Phytochemicals
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UPLC/QTOF MS analysis was performed on Waters ACQUITY I-Class UPLC (Waters, Milford, MA, USA), which was equipped with a binary solvent manager, a sample manager, and a column manager. The mobile phase consisted of acetonitrile (B) and water containing 0.1% formic acid (A) following a gradient elution program: 0–2 min: 0%–2% (B); 2–22min: 2%–60% (B); 22–24min: 60%–90% (B); 24–29 min: 90% (B); 29–30 min: 90%–0% (B); 30–35min: 0% (B). The flow rate was set at 0.4 mL/min 2 μ L of the test solution was injected for UPLC analysis. High-accuracy mass spectrometric data were recorded on a Waters Xevo G2-S QTOF mass spectrometer (Waters, Manchester, UK). Data acquisition was controlled by MassLynx V4.1 software (Waters Corporation, Milford, USA). Automatic metabolite characterization was performed using UNIFI 1.8 (Waters, Milford, USA) by the search of the TCM library. The specific results were shown in Supplementary Fig. 1 and Supplementary Table 1 .
9
MSE Data Processing for Metabolomics Analysis
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All MSE data were collected and processed using UNIFI 1.8 (Waters Corp., Milford, MA, USA). Data within UNIFI 1.8 were passed through the apex peak detection and alignment processing algorithms. The intensity of each ion was normalized with respect to the total ion count to generate a data matrix having RT, m/z value, and the normalized peak area. Charged species, salt adducts, and fragments were all automatically aligned and grouped. The three-dimensional data, including peak number (RT-m/z pair), sample name, and normalized peak areas, were exported to the EZinfo software 3.0.3 (UMETRICS) for PCA. The processed data were also entered into the MetaboAnalyst website (http://www.metaboanalyst.ca ) to perform HCA.
10
MNPs Characterization via Multimodal Spectroscopy
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The morphology and Energy Dispersive X-Ray (EDX) spectroscopies of MNPs were obtained by the scanning electron microscopy (SEM, JSM-6460LV, Japan). Fourier transform infrared spectroscopy (FT-IR, IFS 66 V/S, Germany) was performed to identify the materials with KBr. Other characteristics were measured by vibrating sample magnetometry (VSM, MPMS XL, USA) at room temperature and a D8 advance X-ray diffractometer (XRD, D8, Germany) with Cu Kα radiation (λ = 1.5406 Å). The UPLC–MS/MS analyses were performed by a Waters ACQUITY UPLC system (Waters Corp., Milford, USA) coupled to a triple quadrupole (TQ) mass spectrometer equipped with the electrospray ionization (ESI) source in multiple reactions monitoring (MRM) mode. A Q-TOF SYNAPT G2-S High Definition Mass Spectrometer coupled to ESI (Waters Crop., Manchester, UK) was adopted for detection of ginsenosides metabolites before and after treatment with Fe3O4@SiO2@PDA NPs. The C18 column (50 mm × 2.1 mm, 1.9 μm; Thermo scientific) was employed in the entire experiments. MassLynxV4.1 and MarkerLynx Application Manager (Waters Corporation, Milford, USA) and UNIFI 1.8 (Waters, USA) were carried out to process the collected data. And all detailed steps of mass spectrometry analyses were described in Supplementary data (Methods section), including UPLC–MS/MS analysis, Q-TOF analysis and mass spectral data analysis with UNIFITW.
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