Xevo g2 q tof mass spectrometer

Manufactured by Waters Corporation

Sourced in United States, United Kingdom

The Xevo G2 Q-TOF mass spectrometer is a high-resolution, accurate-mass (HRAM) instrument designed for advanced analytical applications. It features a quadrupole time-of-flight (Q-TOF) mass analyzer that provides precise mass measurements and high sensitivity. The Xevo G2 Q-TOF is capable of performing a wide range of mass spectrometry techniques, including qualitative and quantitative analysis of complex samples.

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76 protocols using xevo g2 q tof mass spectrometer

Shotgun Proteomics Workflow for Protein Identification

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Shotgun quantitative label-free proteomics was performed in a nanoACQUITY UPLC system (Waters, Milford, MA, USA) coupled with a Xevo Q-TOF G2 mass spectrometer (Waters, Milford, MA, USA), as previously described [23 (link)]. Spectra were processed, and proteins were identified and quantified with Progenesis QI for Proteomics^® (Nonlinear Dynamics; Waters Corporation; version 4.0) using Apex3D (Waters) for peak detection and searching the Swiss-Prot Human proteomic database, using all the peptides for relative quantification. In order to obtain the preliminary protein dataset, the following parameters were considered: trypsin digestion with a maximum of one missed cleavage; variable modification via oxidation (M) and fixed modification via carbamidomethyl (C); false discovery rate (FDR) less than 4%; and mass error less than 20 ppm. In addition, ion-matching requirements were established to select proteins with at least one ion per peptide, three ions per protein, and one peptide per protein. Then, the final list of proteins was reduced to selected proteins identified by at least two unique peptides and proteins whose presence was detected in at least 60% of the samples.
The software CYTOSCAPE version 3.9.0 was used to build networks of molecular interactions between the identified proteins with the aid of the ClueGo and String applications.

di Flora D.C., Dionizio A., Pereira H.A., Garbieri T.F., Grizzo L.T., Dionisio T.J., Leite A.D., Silva-Costa L.C., Buzalaf N.R., Reis F.N., Pereira V.B., Rosa D.M., dos Santos C.F, & Buzalaf M.A. (2023). Analysis of Plasma Proteins Involved in Inflammation, Immune Response/Complement System, and Blood Coagulation upon Admission of COVID-19 Patients to Hospital May Help to Predict the Prognosis of the Disease. Cells, 12(12), 1601.

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Antibody Fc-Glycan Removal and Fab2 Isolation

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Antibody samples were digested with PNGase F (New England BioLabs, Ipswich, MA) to remove Fc-glycans. Subsequent IdeS (Genovis Inc, Cambridge, MA) digestion separated the Fab2 from the scFc. The samples were acidified by diluting 1:1 with 0.05% TFA (Sigma-Aldrich, St. Louis, MO) and analyzed by LC/MS on a Waters Xevo Q-TOF G2 mass spectrometer (Waters, Milford, MA) coupled to an Agilent (Santa Clara, CA) 1200 capillary HPLC. The deglycosylated subunits were separated over a Waters BEH300 C4, 1.7 µm, (1.0 × 50 mm) column maintained at 80 °C with a flow rate of 65 µl/min. Mobile phases A and B consisted of water with 0.05% TFA, and acetonitrile with 0.05% TFA, respectively. Proteoforms were eluted from the column using a gradient: 2 to 20% B in 0.5 min, 20–40% B in 6 min, and 40–100% B in 4 min. The mass spectrometer was run in positive MS only mode scanning from 800 to 3500 m/z and data was acquired and spectra summed and deconvoluted (MaxEnt1) using Waters MassLynx 4.1 software.

Procopio-Melino R., Kotch F.W., Prashad A.S., Gomes J.M., Wang W., Arve B., Dawdy A., Chen L., Sperry J., Hosselet C., He T., Kriz R., Lin L., Marquette K., Tchistiakova L., Somers W., Rouse J.C, & Zhong X. (2022). Cysteine metabolic engineering and selective disulfide reduction produce superior antibody-drug-conjugates. Scientific Reports, 12, 7262.

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Label-free Proteomic Analysis Pipeline

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Label-free proteomic analysis was performed in a nanoACQUITY UPLC system (Waters, Milford, MA) coupled to a Xevo Q-TOF G2 mass spectrometer (Waters, Milford, MA), as described elsewhere (Lobo, Leite et al. 2015). The nanoACQUITY UPLC system is equipped with a Trap Columm (100Å, 5 µm, 180 µm × 200 mm) and a HSS T3 M-Class type column (analytical column 75 μm × 150 mm; 1.8 μm) (Waters, Milford, MA). ProteinLynx GlobalServer software (PLGS) version 3.03 (Waters, Milford, MA) was used to process and search the LC-MSE continuum data.
Peptides identification and difference in expression among the groups was obtained using the Protein Lynx Global Server (PLGS) software (version 3.03, Waters Co., UK) as described elsewhere (Lima Leite, Gualiume Vaz Madureira Lobo et al. 2014 (link)). The procedures and bioinformatics analysis were performed as described previously (Dionizio, Melo et al. 2018, Dionizio, Melo et al. 2020 ).

Dionizio A., Uyghurturk D.A., Souza Melo C.G., Sabino-Arias I.T., Araujo T.T., Ventura T.M., Martins Perles J.V., Zanoni J.N., Den Besten P, & Rabelo Buzalaf M.A. (2021). Intestinal changes associated with fluoride exposure in rats: Integrative morphological, proteomic and microbiome analyses. Chemosphere, 273, 129607.

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Chemical Stability of Compounds at Various pH Levels

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The chemical stability of compounds 1b, 2b, 2c, 3b and 3c at various pH (6.2, 6.6, 7.0 and 7.4) was measured on a Waters XEVO QTOF G2 Mass Spectrometer (Waters, Etten-Leur, The Netherlands), with an Acquity H-class solvent manager, Flow-Through Needle (FTN) sample manager and Tunable UV (TUV) detector. The system was equipped with a reversed phase C18 column (Waters, Etten-Leur, The Netherlands, acquity PST 130A, 1.7 µm 2.1 × 50 mm i.d.), with a column temperature of 40 degrees. Mobile phases consisted of 0.1% formic acid in water and 90% acetonitrile. FTN-purge solvent was 5% acetonitrile in water. Mobile phase gradient was maintained starting with 5% acetonitrile to 50% acetonitrile for 15 min at a 220-nm wavelength. Stock solutions of compounds were prepared in DMSO and each sample was incubated at a final concentration of 1–5 μM in pre-thermostated buffered solution. The final DMSO concentration in the samples was kept at 1%. The samples were maintained at 37 °C in a temperature-controlled shaking water bath (60 rpm). At various time points, 100-μL aliquots were removed and injected into the High-Performance Liquid Chromatography (HPLC) system for analysis. Mass was measured in positive sensitivity mode with a mass range between 100 and 1000 Da.

Anduran E., Aspatwar A., Parvathaneni N.K., Suylen D., Bua S., Nocentini A., Parkkila S., Supuran C.T., Dubois L., Lambin P, & Winum J.Y. (2020). Hypoxia-Activated Prodrug Derivatives of Carbonic Anhydrase Inhibitors in Benzenesulfonamide Series: Synthesis and Biological Evaluation. Molecules, 25(10), 2347.

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Proteomic Analysis of Metal-Induced Changes

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Protein spots differentially expressed in the presence of Cu and/or Mn were extracted from the gels with the aid of a scalpel, cut into segments of approximately 1 mm³, transferred to microtubes containing 1 mL of 5% acetic acid (v/v) and subjected to the following steps: dye removal, protein reduction and alkylation and tryptic digestion using 10 ng mL.¹ trypsin solution. The tryptic digestion of the spots was performed using a specific commercial kit (In-GelDigestZP Kit). The peptide sequences in the extracts obtained by the tryptic digestion process were characterized by liquid chromatography tandem mass spectrometry (LC‒MS/MS). Aliquots of the eluted peptide solutions were analyzed using the nanoAcquity UPLC system coupled to the Xevo Q-TOF G2 mass spectrometer (Waters, Manchester, UK) with electrospray ionization system (Waters, UK), which was equipped with HSS T3 column (Acquity UPLC HSS T3 column 75 mm × 150 mm; 1.8 µm, Waters) and operated in positive ion mode. The data obtained were processed using Protein Lynx Global Server (PLGS) version 3.0 and the UniProt databases were used to identify proteins^{34 (link),39 (link)}.

Aparecida Martins R., de Almeida Assunção A.S., Cavalcante Souza Vieira J., Campos Rocha L., Michelin Groff Urayama P., Afonso Rabelo Buzalaf M., Roberto Sartori J, & de Magalhães Padilha P. (2024). Metalloproteomic analysis of liver proteins isolated from broilers fed with different sources and levels of copper and manganese. Scientific Reports, 14, 4883.

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Deglycosylation and Reduction of Protein Samples

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Protein samples were deglycosylated by PNGase F (New England BioLabs, Ipswich, MA) or IgGZero (Genovis, Cambridge MA) according to manufacturer’s recommendation and further reduced by TCEP (Thermo Fisher, Waltham, MA). The samples were acidified by diluting 1:1 with 0.1% formic acid (Sigma-Aldrich, St Louis, MO) followed by liquid chromatography mass spectrometry analysis (LC-MS). LC-MS analysis was performed using a Waters Xevo Q-TOF G2 mass spectrometer (Waters, Milford, MA) coupled to an Agilent (Santa Clara, CA) 1100 capillary HPLC. The deglycosylated and reduced samples were separated over an Agilent Poroshell 300SB-C8 (0.5 × 75 mm) column maintained at 80 °C with a flow rate of 20 µl/min. Mobile phase A was water with 2% acetonitrile and 0.1% formic acid, and mobile phase B was acetonitrile with 2% water and 0.1% formic acid. The mass spectrometer was run in positive MS only mode scanning from 800 to 2000 m/z and data was acquired with MassLynx (Waters) 4.1 software. The TOF-MS signal was summarized and deconvoluted using MaxEnt1 (Waters) program.

Weng Y., Ishino T., Sievers A., Talukdar S., Chabot J.R., Tam A., Duan W., Kerns K., Sousa E., He T., Logan A., Lee D., Li D., Zhou Y., Bernardo B., Joyce A., Kavosi M., O’Hara D.M., Clark T., Guo J., Giragossian C., Stahl M., Calle R.A., Kriz R., Somers W, & Lin L. (2018). Glyco-engineered Long Acting FGF21 Variant with Optimal Pharmaceutical and Pharmacokinetic Properties to Enable Weekly to Twice Monthly Subcutaneous Dosing. Scientific Reports, 8, 4241.

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Peptide Characterization by UPLC-MS, HPLC, and MALDI-TOF

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UPLC-MS was performed on a Waters XEVO QTOF G2 Mass Spectrometer, with an Acquity H-class solvent manager, FTN-sample manager and TUV-detector. The system was equipped with a reversed phase C18-column (Waters, Acquity PST 130A, 1.7 μm 2.1 × 50 mm i.d.), column temperature 40°. Mobile phases consisted of 0.1% formic acid in water (solvent A) and in 90% acetonitrile (solvent B). FTN-purge solvent was 10% acetonitrile in water. Gradient condition: 10%–55% solvent B over 15 min monitored at 220 nm.
Semi-Preparative reversed-phase HPLC was performed on a Waters Delta Prep System equipped with a Waters 2487 Absorbance Detector, using a Vydac C-18 column (250 × 10 mm, 10 μm). A linear gradient of acetonitrile in water/0.1%TFA was used to elute the peptide. Flowrate was 12 mL/min. Finally, Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI TOF)-MS was performed on an Applied Biosystems 4800 MALDI TOF/TOF system in reflector mode using α-cyano-4-hydroxycinnamic acid as matrix material. Both peptides were isolated as single peaks in the LC/MS analysis with VEGF-TAMRA giving an observed mass of 664.34 [M+4H]⁴⁺ (expected 664.53) and VEGF-TAMRA-alk giving an observed mass of 678.57 [M+4H]⁴⁺ (expected 678.79), with m/z ratios resulting in a monoisotopic mass of 2652.28 (expected 2652.33) and 2709.28 (expected 2709.35), respectively.

Yao T., Chen H., Wang R., Rivero R., Wang F., Kessels L., Agten S.M., Hackeng T.M., Wolfs T.G., Fan D., Baker M.B, & Moroni L. (2022). Thiol-ene conjugation of VEGF peptide to electrospun scaffolds as potential application for angiogenesis. Bioactive Materials, 20, 306-317.

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Proteomic Analysis of Biological Samples

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The label-free proteomic analysis was performed in a nanoACQUITY UPLC system (Waters, Milford, MA, USA) coupled to a Xevo Q-TOF G2 mass spectrometer (Waters, Milford, MA, USA). The nanoACQUITY UPLC system was equipped with a Trap Columm (100 Å, 5 μm, 180 μm × 200 mm) and a HSS T3 M-Class type column (analytical column 75 μm × 150 mm; 1.8 μm) (Waters, Milford, MA, USA). The reading and identification of peptides was performed using the ProteinLynx GlobalServer software (PLGS) version 3.03 (Waters, Milford, MA, USA), as previously described [63 (link)]. The PLGS software, applying the Monte-Carlo algorithm, was used to determine the difference in protein expression between the groups, considering p < 0.05 for downregulated proteins and 1 − p > 0.95 for upregulated proteins. The identification of proteins was performed by downloading UniProt databases. Then, bioinformatics analyses were performed using Cytoscape^® 3.6 (Java^®) with the ClusterMarker plugin for the PPI network, and for the determination of the biological process groups based on Gene Ontology annotations, we used the ClueGO plugin [64 (link)].

Souza-Monteiro D., Guerra M.C., Bittencourt L.O., Aragão W.A., Dionizio A., Silveira F.M., Buzalaf M.A., Martins M.D., Crespo-Lopez M.E, & Lima R.R. (2022). Salivary Glands after Prolonged Aluminum Exposure: Proteomic Approach Underlying Biochemical and Morphological Impairments in Rats. International Journal of Molecular Sciences, 23(4), 2251.

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UPLC-MS Analysis of Nanobody Conjugates

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The CPP conjugates were analyzed by UPLC-MS. UPLC-MS was performed on a XEVO QTOF G2 Mass Spectrometer (Waters, Herts, United Kingdom), with an Acquity H-class solvent manager, FTN-sample manager and TUV-detector. The system was equipped with a reversed phase C18-column (Waters, acquity PST 130 A, 1.7 µm 2.1 mm × 50 mm i.d.), column temperature 40 °C. Mobile phases consisted of 0.1 v/v% formic acid in H₂O (buffer A) and 0.09 v/v% formic acid in 10 v/v% H₂O in CH₃CN (buffer B). FTN-purge solvent was 5 v/v% CH₃CN in H₂O. Absorption was measured at 220 nm. For the Atto532-conjugated compounds, a linear gradient of 20–80% buffer B in buffer A over 10 min was used. The DTPA-conjugates were analyzed with a linear gradient of 10–55% buffer B in buffer A over 15 min. Mass was measured in positive sensitivity mode; for a mass range between 400 and 1600 Da or 800 and 1600 Da for DTPA- or Atto532-conjugated nanobodies, respectively. Mass Spectra were deconvoluted using the MaxEnt3 software (Waters), and plotted in R.

Collado Camps E., van Lith S.A., Frielink C., Lankhof J., Dijkgraaf I., Gotthardt M, & Brock R. (2021). CPPs to the Test: Effects on Binding, Uptake and Biodistribution of a Tumor Targeting Nanobody. Pharmaceuticals, 14(7), 602.

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UPLC-MS Analysis of Metabolites

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UPLC/MS analysis was performed on a UPLC system coupled with XEVO G2 Q-TOF mass spectrometer via an ESI source (Waters Corp., Milford, MA). For UPLC separation, 2 μL of sample solution was injected into an ACQUITY HSS T3 C₁₈ column (100 × 2.1 mm, 1.7 μm, Waters). The mobile phase consisted of ACN (A) and water containing 0.1% (v/v) formic acid (B). Linear gradient elution was applied (0–5 min, 5–30% A; 5–10 min, 30–40% A; 10–20 min, 40–65% A; 20–25 min, 65–90% A) at a flow rate of 0.4 mL/min. The column temperature was 45°C. For MS detection, accurate mass was maintained by the LockSpray interface of sulfadimethoxine (309.0658 [M-H]⁻). The operating parameters in negative ion mode were as follows: capillary voltage, 3.0 kV; cone voltage, 30 V; desolvation gas flow rate, 750 L/h; source temperature, 120°C; desolvation temperature, 350°C. MS data were acquired in centroid mode and processed by MassLynx software (Waters, version 4.1).

Song W., Jiang W., Wang C., Xie J., Liang X., Sun Y., Gong L., Liu W, & Qu L. (2019). Jinmaitong, a Traditional Chinese Compound Prescription, Ameliorates the Streptozocin-Induced Diabetic Peripheral Neuropathy Rats by Increasing Sciatic Nerve IGF-1 and IGF-1R Expression. Frontiers in Pharmacology, 10, 255.

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