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Xcalibur software suite

Manufactured by Thermo Fisher Scientific
Sourced in United States, Germany

The XCalibur software suite is a comprehensive data acquisition, processing, and reporting solution designed for Thermo Fisher Scientific's mass spectrometry instruments. It provides a user-friendly interface for instrument control, data management, and advanced data analysis. The core function of the XCalibur software is to enable efficient and reliable data collection, processing, and reporting for mass spectrometry applications.

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4 protocols using xcalibur software suite

1

Extraction and Analysis of Plant Waxes

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The first leaves of 14-d-old plants and spikes from mature plants were dipped twice into 99% HPLC molecular-grade chloroform for 15 s and then 10 s, an internal standard of 0.5 μg.mL–1 tetracosane (C24n-alkane) was then added. Lemma awns were trimmed from the spikes prior to the analysis. Solvent was removed from the wax extracts under a gentle stream of N2. Wax residues were derivatised using N,O-bis(trimethylsilyl)trifluoroacetamide + 1% trimethylcholorosilane (BSTFA + 1% TMCS; Sigma-Aldrich) and excess reagent removed again under N2. The wax constituents were identified by their electron-impact mass spectra (70 eV, m/z 50–950) after capillary GC (Restek Rxi-1HT, 15 m × 0.32 mm, 0.1 μm [Thames Restek Ltd.]) performed on an ISQ-LT GC–MS comprising a 1300 gas chromatograph combined with a single quadrupole mass analyser (Thermo-Fisher Scientific). The samples were injected onto the analytical column at 50 °C, ramping at 0.2 °C s–1 to a maximum of 380 °C, where it was held for 7 min. The flow rate of the He carrier gas was 5 mL min–1. All data were acquired using the XCalibur software suite (Thermo Fisher Scientific). Leaf area and spike length were calculated using ImageJ87 (link).
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2

Mass Spectrometry Data Analysis

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All data were analyzed using the XCalibur software suite (Thermo Scientific, Waltham, MA, USA). Ion chronograms and mass spectra were converted into text files and analyzed with Excel (Microsoft, Redmond, WA USA).
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3

Nano-ESI-MS Characterization of Biomolecules

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Nano electrospray-ionization mass spectrometric experiments were performed on an LTQ Orbitrap XL instrument (Thermo Fisher Scientific, Bremen, Germany) with Econo12 Glass PicoTips (New Objective, Littleton, MA, USA) as electrospray emitters. Mass spectrometry was performed in positive ionization mode with spray voltages ranging from 0.8 to 1.3 kV, tube lens voltage of 250 V, capillary voltage of 20 V, and a capillary temperature of 200 °C. The mass spectrometer was used in FTMS mode at a resolution of 100,000. HCD experiments were performed with precursor ion isolation windows in the range of 3 to 8 m/z. Collision energies ranged between 0% and 50% NCE and were converted to eV [45 (link),46 (link)]. Data processing was performed using the Xcalibur software suite (Thermo Fisher Scientific, Bremen, Germany).
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4

Charge State Analysis of Proteins

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The XCalibur software suite (Thermo Scientific, San Jose, CA) was used for data analysis. From the mass spectrum of each protein, the intensity-weighted average charge state (qave) was calculated according to Equation 1, in which qi was the net charge of the ith charge state, Ii was the signal intensity of the corresponding ith charge state, and N was the total number of the observed protein charge states in the spectrum.
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