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8 protocols using ms grade

1

Peptide Analysis by LC-MS/MS

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All excised and digested bands were analyzed by LC⿿MS/MS. Peptides were chromatographically separated using the EASY-nLC II system (Thermo, Germany) with a 2 column set up: trap column C18-A1, 2 cm (Thermo, Germany) and analytical column PepMap C18, 15 cm ÿ 75 μm, 3 μm particles, 100 ÿ pore size (Thermo, Germany). Mobile phases used were A: 0.1% formic acid in water and B: 0.1% formic acid in acetonitrile. All solvents used were MS grade (Sigma, Germany). Total of 2 μL of each sample was loaded and separated by a gradient over the course of 80 min with a flow rate of 300 nL/min. The flow gradient was (i) 0⿿5 min at 5% B, (ii) 5⿿55 min, 5⿿70% B, (iii) 55⿿60 min 70⿿95% B, (iv) 60⿿70 min 95% B, (v) 70⿿75 min 95⿿5% B, (vi) 75⿿80 min 5% B.
Peptides were analyzed by LTQ Orbitrap XL mass spectrometer in data dependent mode with nano-ESI spray voltage of 1.9 kV, capillary temperature of 275 °C and tube lens value set at 110 V. All spectra were acquired in positive mode with high-resolution full scan in the mass range m/z 300⿿2000 and Orbitrap resolution of 30,000. The 5 most intense precursors were subjected to collision induced dissociation (CID) with normalized collision energy of 35 and activation time of 30 ms. Dynamic exclusion with 1 repeat count over 10 s and exclusion for 10 s was applied.
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2

Synthesis and Characterization of 18 OH-PCB Standards

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In this
study 18 OH-PCB standards were used
(Table S1): 4′-OH-CB35, 4′-OH-CB79,
4,4′-diOH-CB80, 4′-OH-CB127, 4,4′-diOH-CB111,
4-OH-CB130, 4-OH-CB193, 4′-OH-CB30, 2-OH-CB77, 4-OH-CB107,
4,4′-diOH-CB83, 4′-OH-CB159, 4-OH-CB172, 4′-OH-CB120,
4,3′-diOH-CB90, 4-OH-CB108, 4,2′-diOH-CB107 and 4,3′-diOH-CB107.
All OH-PCB standards were synthesized at Stockholm University, Department
of Environmental Chemistry (current Department of Environmental Science),
as described by Bergman et al.24 (link)For flow injection analysis, the water phase used was prepared from
ultra high purity water (Riedel de Haën, HPLC grade, Germany)
and ammonium bicarbonate (Sigma-Aldrich, MS grade, Germany). The pH
of the buffer was adjusted to 8.0 with ammonia (Merck, 25%, MS grade,
Canada). Acetonitrile (Rathburn, S-grade, Scottland) was used as the
organic component of the mobile phase.
Theophylline, polyalanine
4–7, sulfaguanidine, sulfadimethoxine,
and val-tyr-val all in Major Mix IMS/ToF Calibration Kit (Waters Corporation,
U.K.) as well as lauric acid, linolenic acid, cholate (kindly donated
by Miklós Mohai from the Stockholm University and Jaanus Liigand
from the University of Tartu) were analyzed together with the OH-PCBs
for calibration of the cyclic IMS measurements (CCS values vs drift
time).
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3

Characterization of Lavender Oil Samples

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As the aim of this study was to rapidly assess the lavender oils received by essential oil distributors for the purpose to characterize and grade oils of varying quality, a distributor provided 54 lavender oil samples for characterization. Of these, 30 originated from France/Bulgaria and 24 originated from Indonesia/Cambodia. Nine additional oils of unknown origin (unclassified samples) were also provided for analysis.
Each sample was prepared by diluting 20 µL into 2.0 mL hexane (MS Grade, Sigma Aldrich, Castle Hill, NSW, Australia). A 50 ppm C8-C22 mixed alkane standard (Fluka, Castle Hill, NSW, Australia) was used as an internal standard. Each sample was analyzed in in triplicate and reported as the average response.
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4

HILIC-HRAM Metabolite Profiling of Sweat Samples

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All sweat samples, pooled samples, standard curves, and blanks (2 μL injections) were separated via hydrophilic interaction liquid chromatography (HILIC) on a Vanquish Horizon UPLC system paired with high resolution accurate mass (HRAM) detection on a Q-Exactive HF mass spectrometer (Thermo Fisher Scientific). Separations were performed at 170 μL min−1 using a Waters Acquity BEH Amide column (130 Å, 1.7 μm, 2.1 × 100 mm) with mobile phase A consisting of 10 mM ammonium formate in 4.5% acetonitrile (aq) and mobile phase B consisting of 10 mM ammonium formate in 95.5% acetonitrile (aq) (MS grade, ≥99.0%, Sigma Aldrich, St. Louis, MO, USA). A 30-min gradient of mobile phases was run, beginning with 90% mobile phase B for 5 min. The percent B transitioned to 65% at 18.5 min and held at 65% for 5 min (23.5 min). The gradient returned to 90% B at 24.5 min and remained at 90% B for the remainder of the run. The mass spectrometer source was operated in positive ionization mode with 3.5 kV spray voltage, 250°C capillary temperature, and sheath gas of 30. The intact mass scans (MS1 only) were acquired at 60,000 resolution over a 65–400 m/z range (profile) with a 1 × 106 AGC target and a 50 ms maximum ion accumulation time.
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5

Quantitative Analysis of Habanero Chili Compounds

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Habanero chili (Capsicum chinense) seeds (CPS) were obtained from Italmesa Company, Puebla, Mexico. Celuzyme (Cellulase, 121,000 UI/kg) was kindly donated by Enmex S.A. de C.V., Estado de Mexico, Mexico. Capsaicin (> 97%, M2028) used as standard in the HPLC quanti cation, HPLC grade water and methanol, and analytical grade formic acid were purchased from Sigma (St. Louis, MO, USA). The solvents used for the UPLC-MS analysis were MS grade and purchased from Sigma-Aldrich (St. Louis, MO, USA). 60 phenolic standards were obtained for quanti cation as is described in Juarez-Trujillo et al.
(2018) and all the stock solutions, samples, solvents and reagents were ltered through 0.20 µm PTFE membrane lters (Phenomenex, USA) before injection in the analytical platform [12] (link). For the in vitro experiments Dulbecco's Modi ed Eagle Medium (DMEM; Gibco, Gaithersburg, MD, USA), fetal bovine serum (FBS; GenDEPOT, Barker, TX, USA) and penicillin-streptomycin antibiotics were purchased. Finally, murine macrophage cell line (RAW 264.7) was obtained from American Type Cell Collection (ATCC, Manassas, VA, USA).
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6

Solvents and Reagents for Mass Spectrometry

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Acetonitrile and methanol (MS grade) were purchased from Merck (Darmstadt, Germany) and Burdick and Jackson (Ulsan, Korea), respectively. Formic acid was purchased from Sigma-Aldrich Co. (St. Louis, USA). Ultrapure water was purified by a Milli-Q water purification system (Millipore, Bedford, MA). Other chemicals were of analytical grade.
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7

Protein Extraction and Trypsin Digestion

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Single colonies (diameter >2 mm) were picked using a micropipette tip or a 10 μL loop, and resuspended in 200 μL of 50 mM ammonium bicarbonate (MS grade; Merck, Germany), sonicated for 1 min (3 s of sonication, 6 s of rest), centrifuged at 12,000 × g for 2 min and heated at 95°C for 5 min, after which the buffer was removed using 10K Nanosep centrifugal device with Omega membrane (Pall Corporation, Port Washington, NY, United States). Ammonium bicarbonate buffer (50 mM) was added along with sequencing grade trypsin (Promega Corporation, Madison, WI, United States), and the solution was microwaved in a water bath followed by heat treatment at 55°C. The peptide concentration was measured using the Pierce™ Quantitative Colorimetric Peptide Assay kit (Thermo Fisher Scientific, Waltham, MA, United States).
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8

UHPLC-OrbiTrap Mass Spectrometry Protocol

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UHPLC separation was carried out on an Accela 600 system coupled to the LTQ OrbiTrap XL mass spectrometer (ThermoFisher Scientific, Bremen, Germany). The analytical column used for separation was a Syncronis C18 column (100 × 2.1 mm, 1.7 µm) heated to 40 °C. The mobile phase was composed of (A) 0.1% formic acid (MS grade, Sigma-Aldrich, Steinheim, Germany) and (B) acetonitrile (MS grade, Merck, Darmstadt, Germany) with 0.1% formic acid. The flow rate was set to 0.175 mL min−1 and the gradient elution program was previously described by Banjanac et al. [32 (link)]. MS parameters of the ion source and the other MS settings were as previously described in Banjanac et al. [32 (link)].
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