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Tracefinder 4.1 clinical

Manufactured by Thermo Fisher Scientific
Sourced in United States

TraceFinder™4.1 Clinical is a software solution for clinical research and routine analysis. It provides data processing, reporting, and review capabilities for targeted and untargeted quantitative and qualitative analysis of samples.

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4 protocols using tracefinder 4.1 clinical

1

Quantifying Cone Hormone Profiles

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Hormone contents in three biological replicates of male cones (M3-5), female cones (F3-5), and bisexual cones (BM4-5 and BF4-5) were quantified, with a minimum of 5 buds per biological replicate. Purification of ~100 mg of frozen plant material samples utilized C18 reversed-phase, polymer-based, solid-phase extraction (RP-SPE) cartridges, followed by analysis on a UPLC– Orbitrap-MS system (UPLC, Vanquish; MS, QE) and a Q Exactive hybrid Q–Orbitrap mass spectrometer equipped with a heated ESI source (Thermo Fisher Scientific Inc., USA). Data acquisition employed Q-Exactive with Xcalibur 4.1 (Thermo Fisher Scientific Inc., USA) and processing utilized TraceFinder™4.1 Clinical (Thermo Fisher Scientific Inc., USA). All experiments were conducted at BioNovoGene (Suzhou, China). The measured hormone concentrations included IAA, salicylic acid (SA), gibberellins (GA1, GA3, GA4, GA7), abscisic acid (ABA), jasmonic acid (JA) and jasmonic acid-isoleucine (JA-Ile).
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2

UHPLC-ESI-MS/MS Analysis of Acid-Digested Samples

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The sample was digested with 2 M HCl at 80 °C for 3 h. An aliquot (200 μL) of the supernatant was evaporated under a gentle stream of N2. For UHPLC-ESI-MS/MS analysis, the samples were dissolved in 1 mL of 30 % methanol (vol/vol) and transferred to insert-equipped vials. The sample extracts were analysed using an UPLC-Orbitrap-MS system (UPLC, Vanquish; MS, QE). The analytical conditions were as follows, UPLC: column, Waters ACQUITY UPLC HSS T3 (1.8 μm, 2.1 mm × 50 mm); column temperature, 40℃; flow rate, 0.3 mL/min; injection volume, 2 μL; solvent system, water (0.1 % formic acid): acetonitrile (0.1 % formic acid); gradient program, 90:10 V/V at 0 min, 90:10 V/V at 1.0 min, 65:35 V/V at 6 min, 5:95 V/V at 8 min, 5:95 V/V at 10 min, 90:10 V/V at 10 min, 90:10 V/V at 12 min. HRMS data were recorded on a Q Exactive hybrid Q-Orbitrap mass spectrometer equipped with a heated ESI source (Thermo Fisher Scientific) using SIM MS acquisition methods. The ESI source parameters were set as follows: spray voltage, −2.8 kV; sheath gas pressure, 40 arb; aux gas pressure, 10 arb; sweep gas pressure, 0 arb; capillary temperature, 320 ℃; and aux gas heater temperature, 350 ℃. Data were acquired on Q-Exactive by using Xcalibur 4.1 (Thermo Scientific), processed using TraceFinder™4.1 Clinical (Thermo Scientific). Quantified data were output into Excel format.
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3

Quantitative Proteomic Analysis Pipeline

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Data were acquired on the Q-Exactive Plus using Xcalibur 4.1 (Thermo Scientific) and the ChipMate 8.3.3 software (Advion), and processed using TraceFinder 4.1 Clinical (Thermo Scientific). Data were acquired on the TQD MS/MS using MassLynx (Waters) and these data were processed using Neolynx (Waters). Quantified data were output into excel format, and analysis and visualization were performed using R version 3.4.3 [28 ].
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4

Quantitative Analysis of Amino Acids via UPLC-Orbitrap MS

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Fifty milligrams of the sample was accurately weighed into a centrifuge tube, and 0.5 ​mL of 0.1 ​M hydrochloric acid, vortexed, and extracted for 1 ​h at room temperature. The samples were centrifuged at 12000 ​rpm for 10 ​min, and the supernatant was collected. A 10 ​μL sample was placed into a bottle, and 70 ​μL of AccQ•Tag Ultra Borate buffer and 20 ​μL of AccQ•Tag reagent were added. The reaction mixture was heated at 55 ​°C for 10 ​min and then tested on a computer after cooling. The sample extracts were analyzed using a UPLC–Orbitrap-MS system (UPLC, Vanquish; MS, QE). HRMS data were recorded on a Q Exactive hybrid Q–Orbitrap mass spectrometer equipped with a heated ESI source (Thermo Fisher Scientific) utilizing the SIM MS acquisition methods. Data were acquired on the Q-Exactive using Xcalibur 4.1 (Thermo Scientific) and processed using TraceFinder™4.1 Clinical (Thermo Scientific).
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