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5 protocols using milli q water ddh2o

1

MALDI-MRMS Imaging Mass Spectrometry

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All reagents were of HPLC grade. Milli-Q water (ddH2O; Millipore) was prepared in-house. Conductive indium tin oxide (ITO)-coated glass slides were purchased from Bruker Daltonics (Bremen, Germany). Adhesive slides SuperFrost PlusTM were obtained from Thermo Fisher Scientific (Waltham, Massachusetts, USA) for histological analysis. Trifluoroacetic acid (TFA) and 1,5-diaminonaphtalene (1,5-DAN, ≥97.0%) MALDI matrix were purchased from Sigma-Aldrich (St. Louis, MO). 4-phenyl-α-cyanocinnamic acid amide (PhCCAA) matrix was obtained from SiChem (Bremen, Germany). Acetonitrile (ACN) was obtained from VWR (Darmstadt, Germany). For external calibration of the Bruker solarix magnetic resonance mass spectrometer (MRMS), a mixture of poly-DL-alanine (10 mg/mL), L- alanine ≥ 99.5% (5 mg/mL), and taurine ≥ 99% (5 mg/mL; all from Sigma-Aldrich) was used in water.
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2

Lipopolysaccharide Inflammation Assay

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All reagents were of HPLC or cell culture grade. Lipopolysaccharide from Escherichia coli O55:B5 (LPS, Cat. No. L2880) was purchased from Sigma-Aldrich (Taufkirchen, Germany). Phosphate buffer saline (PBS; Biowest, Cat. No. L0615), Acetonitrile (ACN; Merck, Cat. No. 100030), Trifluoracetic acid (TFA; Merck, Cat.Nno. 108262), 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyltetrazoliumbromid (MTT; PanReac AppliChem, Cat. No. A2231) and Dimethylsulfoxide (DMSO; Cat. No. 23500260) were purchased from VWR International (Darmstadt, Germany). Milli-Q water (ddH2O; Millipore) was prepared in-house. Mouse IL-6 and TNF-α ELISA kits (Cat. No. 900-TM50 and 900-TM54) were obtained from PeproTech GmbH (Hamburg, Germany). 2,5-dihydroxybenzoic acid (DHB; Cat. No. 8201346) was purchased from Bruker Daltonics (Bremen, Germany). Brain Total Lipid Extract (TBLE; Cat. No. 131101) was from Avanti Polar Lipids (Alabaster, USA). SAHA (suberoylanilide hydroxamic acid, Vorinostat; Cat. No. 10009929) was purchased from Cayman Chemical (Ann Harbor, USA). ESI-L LC/MS tuning mix (Cat. No. G1969-85,000) was from Agilent (Santa Clara, USA).
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3

HPLC-MS Characterization of Small Molecules

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All reagents were of HLPC grade. Acetonitrile (ACN) and trifluoroacetic acid (TFA) were purchased from Merck (Darmstadt, Germany). Dimethylsulfoxide (DMSO; cell culture grade) was obtained from Sigma Aldrich (Munich, Germany). Milli-Q water (ddH2O; Millipore) was prepared in-house. 2,5-Dihydroxybenzoic acid (DHB), 6-Aza-2-thiothymine (ATT) and the peptide MALDI-MS calibration standard mix (cat. no. # 8222570) were purchased from Bruker Daltonics (Bremen, Germany). Imatinib Free Base (Cat. No. I-5577), Dasatinib Free Base (Cat. No. D-3307), Nilotinib Free Base (Cat. No. N-8207), Vandetanib (Cat. No. V-9402), Sorafenib Free Base (Cat. No. S-8599) and Sunitinib Malate Salt (S-8803) were purchased from LC Laboratories (Woburn, USA); Chloroquine diphosphate salt (Cat. No. C6628) was obtained from Sigma-Aldrich. Olanzapine (Cat. No. S2493) and Romidepsin (Cat. No. S3020) were obtained from SelleckChem.
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4

MALDI-MS Analysis of Amyloid-Beta Peptides

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All reagents were HLPC grade. Acetonitrile (ACN) and Trifluoroacetic acid (TFA) were from Merck (Darmstadt, Germany). Dimethyl sulfoxide (DMSO) was obtained from Sigma-Aldrich (Munich, Germany). Milli-Q water (ddH2O; Millipore, Burlington, USA) was prepared in-house. sDHB (9:1 mixture of 2,5-dihydroxybenzoic acid (DHB) and 2-hydroxy-5-methoxybenzoic acid), the MALDI-MS peptide calibration standard mix II and protein calibration standard mix I were from Bruker Daltonics (Bremen, Germany). Synthetic Aβ1-38, Aβ1-39, Aβ1-40, Aβ1-42, Aβ1-43 and Aβ1-45 were from rPeptide (Watkinsville, USA) and mixed at an equimolar concentration of 2 µmol/L in ddH2O (Aβ calibration standard).
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5

MALDI-MRMS Metabolite Profiling

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All reagents were of HPLC grade. Milli-Q water (ddH2O; Millipore) was prepared in-house.
Conductive indium tin oxide (ITO) coated glass slides were purchased from Bruker Daltonics (Bremen, Germany). Adhesive slides SuperFrost Plus TM were obtained from Thermo Fisher Scientific (Waltham, Massachusetts, USA) for histological analysis. Trifluoroacetic acid (TFA) and 1,5-diaminonaphtalene (1,5-DAN, ≥ 97.0%) MALDI matrix were purchased from Sigma-Aldrich (St. Louis, MO). Acetonitrile (ACN) was obtained from VWR (Darmstadt, Germany). For external calibration of the Bruker solarix magnetic resonance mass spectrometer (MRMS), a mixture of poly-DL-alanine (10 mg/mL), L-alanine ≥ 99.5% (5 mg/mL) and taurine ≥ 99% (5 mg/mL; all from Sigma Aldrich) in water was used.
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