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Waters synapt g2 s

Manufactured by Waters Corporation
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The Waters Synapt G2-S is a high-performance mass spectrometry system designed for advanced analytical applications. It is capable of performing ion mobility separation and time-of-flight mass analysis, providing enhanced separation and detection capabilities for complex samples.

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Lab products found in correlation

Sequencing grade chymotrypsin, by Roche (1 mentions) Automatic injector, by Harvard Apparatus (1 mentions) Proteinlynx global server, by Waters Corporation (1 mentions)

3 protocols using waters synapt g2 s

1

Disulfide Bond Confirmation in rVHs

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For additional disulfide bond introduction, Gly or Ala and Ile at positions 54 and 78 of rVHs were both mutated to Cys by site-directed mutagenesis. Cys introduced mutants were prepared by the same methods as wild type rVHs, and disulfide formations were confirmed for H2-1-1, H3-9, and H3-15 as follows. rVHs and their mutants were treated with sequencing grade chymotrypsin (Roche, Basel, Switzerland) at 37 °C for 4 hours followed by addition of 10% formic acid, and then subjected to LC-MS analysis using a Waters Synapt G2S (Waters Corporation, Milford, MA, USA). Peptide identification was conducted with MassLynx Mass Spectrometry Software ver. 4.1 and BiopharmaLynx Software ver. 1.3 (Waters Corporation).
Shinozaki N., Hashimoto R., Fukui K, & Uchiyama S. (2017). Efficient generation of single domain antibodies with high affinities and enhanced thermal stabilities. Scientific Reports, 7, 5794.
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2

ESI-MS Analysis of Glycosylated Peptides

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Electrospray ionization mass spectrometry experiments were performed on a Waters Synapt G2-S (Waters Coproration, Milford, MA, USA). The solutions were infused at a flow rate of 2 µL/min with an automatic injector (Harvard Apparatus, Holliston, MA, USA). The capillary voltage was set to 2 kV, and the source and desolvation temperature to 80 °C and 120 °C, respectively. Collision-induced dissociation (CID) was performed with Argon as collision gas and electron transfer dissociation (ETD) with para-nitrotoluene as the reagent. CID collision energy was optimized depending on the charge state and the type of fragmentation investigated (around 20 V for the glycosylation and between 40 and 60 V for the peptide). For ETD experiments, the discharge current was set to 50 µA, the makeup gas flow to 90 mL/min and the trap RF offset voltage to 425 V with a refill time was 0.2 s. Trap wave height was set to values between 0.15 and 0.3 to optimize the fragmentation.
Saintmont F., Cazals G., Bich C, & Dutertre S. (2022). Proteomic Analysis of the Predatory Venom of Conus striatus Reveals Novel and Population-Specific κA-Conotoxin SIVC. Toxins, 14(11), 799.
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3

MS/MS Data Preprocessing for RAMM Analysis

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To analyze LC-MS/MS data with RAMM, data must first be converted from its original, vendor specific RAW format to a non-vendor specific format. In this manuscript, RAW refers to a data file format and should be distinguished from actual raw data. RAMM uses the MGF file format as the universal file input format. The MGF format contains the information (precursor m/z, retention time, MS/MS spectral data) needed to perform the MS/MS interpretation. If the MS/MS data is acquired in profile mode, it must also be centroided for use with RAMM. No additional pre-processing of the data (i.e. noise reduction, deisotoping, etc.) is required, but can be performed prior to analysis by RAMM.
To pre-process data generated on the Fusion Lumos, MSConvertGUI (64-bit, proteowizard.sourceforge.net) was used to convert the RAW file to MGF format file. The data acquired in this study was profile data, and MSConvertGUI was also used to convert the profile data to centroid data. To pre-process the data generated on the Waters Synapt G2-S, PLGS (ProteinLynx Global Server, Waters Corp) was used for Lockspray correction of the RAW file, which was exported in mzML format. MSConvertGUI was then used to convert the mzML to MGF format.
Lobue P.A., Yu N., Jora M., Abernathy S, & Limbach P.A. (2018). Improved Application of RNAModMapper – an RNA Modification Mapping Software Tool – for Analysis of Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Data. Methods (San Diego, Calif.), 156, 128-138.
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