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Sinapinic acid matrix

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Sinapinic acid is a chemical compound commonly used as a matrix in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry analysis. It facilitates the ionization and detection of analytes, particularly large biomolecules such as proteins and peptides.

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Lab products found in correlation

Sodium trifluoroacetate, by Thermo Fisher Scientific (2 mentions) Ultraflex 3, by Merck Group (2 mentions) Hplc grade acetonitrile, by Thermo Fisher Scientific (2 mentions) C18 ziptip, by Thermo Fisher Scientific (1 mentions) Hek293a cells, by American Type Culture Collection (1 mentions) Autoflex mass spectrometer, by Bruker (1 mentions) Vivaspin device, by Sartorius (1 mentions) Flexanalysis software, by Bruker (1 mentions) Protein calibration standard 1, by Bruker (1 mentions) Trifluoroacetic acid, by Thermo Fisher Scientific (1 mentions) Hek293a cells, by Thermo Fisher Scientific (1 mentions) Hplc grade water, by Thermo Fisher Scientific (1 mentions) Oregon green 488, by Thermo Fisher Scientific (1 mentions)

5 protocols using sinapinic acid matrix

1

Aβ42 Oxidation Kinetics by MALDI-TOF-MS

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MALDI-TOF-MS measurements were done in a Bruker Voyager instrument using sinapinic acid matrix (Sigma, 10 mg/mL stock containing 1:1 ACN:H2O with 0.1% TFA). Oxidation reactions were initiated by adding 100 μM Asc to 10 μM Aβ42 and 9 μM Cu2+ in 20 mM PBS pH 7.4 in the absence and presence of 90 μM L. Reactions were quenched by 0.1% TFA after 5 min followed by denaturation with 4 M guanidinium hydrochloride (VWR). Samples were purified with C18 ziptips (Fisher) followed by eluting with α-cyano-4-hydroxy cinnamic acid (CHCA) matrix in 60% ACN, 0.1% TFA and directly spotted on the MALDI plate. A minimum allowable intensity laser was used.
Mitra S., Talukdar K., Prasad P., Misra S.K., Khan S., Sharp J.S., Jurss J.W, & Chakraborty S. (2021). Rational Design of a Cu Chelator that Mitigates Cu-Induced ROS Production by Amyloid Beta. Chembiochem : a European journal of chemical biology, 23(4), e202100485.
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2

PAMAM Dendrimer Purification and Characterization

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Biomedical grade G5 PAMAM dendrimer was purchased from Dendritech Inc. and purified using rp-HPLC to give a molecular weight fraction free of trailing generations (G1–G4) as well as G5 dimers and higher oligomers.28 (link) Trifluoroacetic acid, HPLC grade water, GE PD-10 Sephadex columns, and HPLC grade acetonitrile were purchased from Fisher-Scientific and used as received. 5-carboxy tetramethylrhodamine succinimydyl ester (TAMRA) was purchased from Life Technologies. A 500 MHz Varian NMR instrument was used for all 1H and 19F NMR measurements. All MALDI-TOF MS measurements were performed on a Bruker Ultraflex III with sinapinic acid matrix (Sigma Aldrich) and sodium trifluoroacetate (Fischer Scientific) salt sample preparation. Serum-free DMEM (SFM) from life technologies was employed for cell culture of HEK293A cells, which were obtained from ATCC. Complete medium was made by adding 50 mL of fetal bovine serum (FBS) and 5 mL 100× of penicillin streptomycin to 500 mL of SFM.
Dougherty C.A., Vaidyanathan S., Orr B.G, & Banaszak Holl M.M. (2015). Fluorophore:Dendrimer Ratio Impacts Cellular Uptake and Intracellular Fluorescence Lifetime. Bioconjugate chemistry, 26(2), 304-315.
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3

MALDI-TOF Mass Spectrometry Analysis

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MALDI-TOF mass spectra were measured with an Autoflex mass spectrometer (Bruker Daltonics) operated on linear positive ion mode. External mass calibration of the instrument, for the m/z range of interest, was carried out using the monomeric (66.4 kDa) and dimeric (132.8 kDa) molecular ions of BSA (reference 7030; Sigma-Aldrich) as calibrants. Before MS analysis the protein samples (concentration around 10 μM; before and after cross-linking) were submitted to buffer exchange against 20 mM Tris (pH 7.5), 50 mM NaCl, using Vivaspin devices (Sartorius, cut-off of 30 kDa for Impβ alone and 10 kDa for Impβ/Rev). The buffer-exchanged protein samples were then mixed in a 1:2, 1:5 or 1:10 (vol/vol) ratio with sinapinic acid matrix (Sigma-Aldrich; 10 mg/ml in water/acetonitrile/TFA, 50/50/0.1, vol/vol/v) and 1–2 μl were deposited on the target and allowed to air dry at RT. Mass spectra data were processed with flexAnalysis software (v.3.0; Bruker Daltonics).
Spittler D., Indorato R.L., Boeri Erba E., Delaforge E., Signor L., Harris S.J., Garcia-Saez I., Palencia A., Gabel F., Blackledge M., Noirclerc-Savoye M, & Petosa C. (2022). Binding stoichiometry and structural model of the HIV-1 Rev/importin β complex. Life Science Alliance, 5(10), e202201431.
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4

MALDI-TOF-MSI of Mouse Brain Tissue

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Sections of the defined ROIs of the optically cleared and paraffin-embedded mouse brain tissue were dried and adhered by incubating the slide for 1 h at 70 °C. Remaining paraffin was removed with xylene (2 × 3 min) and the slides were washed with 2-propanol (3 min). For tissue rehydration, slides were incubated in ethanol dilutions decreasing from 100%, 90%, 70%, 50% to 30% (1 min, each). Following evaporation of ethanol at 40 °C, 10 g/l sinapinic acid matrix (Sigma-Aldrich) in 60% acetonitril/0.2% trifluoroacetic acid was deposited onto the sections using an ImagePrep automated sprayer (Bruker Daltonics). MALDI-TOF-MSI was carried out in linear positive ion mode over a mass range of m/z 2.5–25 kDa. The lateral resolution was set to 50 μm. The Smartbeam-II Nd:YAG (355 nm) laser frequency was set to 200 Hz with 300 shots per spot and a sample rate of 0.50 GS/s. External calibration was performed with Protein Calibration Standard I (Bruker) mixed 1:1 (v/v) with matrix solution and spotted onto the slide.
Blutke A., Sun N., Xu Z., Buck A., Harrison L., Schriever S.C., Pfluger P.T., Wiles D., Kunzke T., Huber K., Schlegel J., Aichler M., Feuchtinger A., Matiasek K., Hauck S.M, & Walch A. (2020). Light sheet fluorescence microscopy guided MALDI-imaging mass spectrometry of cleared tissue samples. Scientific Reports, 10, 14461.
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5

PAMAM Dendrimer Synthesis and Purification

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Biomedical grade G3 PAMAM dendrimer with ethylenediamine core was purchased from Dendritech Inc. and purified using rp-HPLC to give a molecular weight fraction free of trailing generations, dimers and higher oligomers.23 Trifluoroacetic acid, HPLC grade water, GE PD-10 sephadex column, and HPLC grade acetonitrile were purchased from Fisher-Scientific and used as received. Oregon Green 488 was purchased from Life Technologies. A 500 MHz Varian NMR instrument was used for all 1H NMR measurements. All MALDI-TOF MS measurements were performed on a Bruker Ultraflex III with sinapinic acid matrix (Sigma-Aldrich) and sodium trifluoroacetate (Fischer Scientific) salt sample preparation. Serum-free DMEM (SFM) and RPMI from life technologies was employed for cell culture of HEK 293A cells, which were obtained from Life Technologies. Complete media was made by adding 50 mL of fetal bovine serum (FBS) and 5 mL of 100× of penicillin–streptomycin to 500 mL of SFM.
Vaidyanathan S., Kaushik M., Dougherty C., Rattan R., Goonewardena S.N., Banaszak Holl M.M., Monano J, & DiMaggio S. (2016). Increase in Dye:Dendrimer Ratio Decreases Cellular Uptake of Neutral Dendrimers in RAW Cells. ACS biomaterials science & engineering, 2(9), 1540-1545.
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