Dithiothreitol (DTT), iodoacetamide (IAA), formic acid (LC-MS grade), Na
2HPO
4, and NaH
2PO
4 were purchased from Thermo Fisher Scientific (Waltham, MA). Ammonium bicarbonate (ABC) buffer (50 mM) was freshly prepared from a 500 mM stock solution.
LC-MS grade water and
acetonitrile were purchased from Honeywell (Charlotte, NC).
Trypsin gold and rLys-C (MS grade) were from Promega (Madison, WI). Scott’s tap water substitute bluing reagent was from Ricca Chemical (Arlington, TX). Ethanol was purchased from Decon Laboratories, King of Prussia, PA, and paraffin wax was from Blended Waxes, Inc. (Oshkosh, WI). Other chemicals were from Sigma-Aldrich (St. Louis, MO). Neutral buffered formalin (pH 6.8–7.0) was prepared by combining 25 mL (37–40% w/w) of formaldehyde with 225 mL of purified water, 1.0 g of NaH
2PO
4, and 1.625 g of anhydrous Na
2HPO
4. Carboxymethylcellulose solution (CMC; 2.5% w/v in water) was prepared for embedding fresh samples prior to freezing. A stock solution of
n-dodecyl-
β-
d-maltoside (DDM, Sigma-Aldrich), a nonionic surfactant used for protein extraction and solubilization,
36 (link) was prepared at 1% (w/v) in water and further diluted for use, as described below. Nanowell chips were fabricated as described previously.
17 (link)
Nwosu A.J., Misal S.A., Truong T., Carson R.H., Webber K.G., Axtell N.B., Liang Y., Johnston S.M., Virgin K.L., Smith E.G., Thomas G.V., Morgan T., Price J.C, & Kelly R.T. (2022). In-Depth Mass Spectrometry-Based Proteomics of Formalin-Fixed, Paraffin-Embedded Tissues with a Spatial Resolution of 50–200 μm. Journal of proteome research, 21(9), 2237-2245.