Chipsoft 8

The masses of the important cyclic peptides were determined at high resolution (Supplementary Note 2). High-resolution mass spectrometry (HR-MS) analyses were performed on the Exploris 240 mass spectrometer (Thermo Fisher Scientific) interfaced with a chip-based nanoESI source (TriVersa Nanomate, Advion Biosciences), controlled by Chipsoft 8.3.1 software (Advion Biosciences). Samples were prepared in a solution of MeCN:H₂O:HCOOH (50:49.9:0.1) at a final concentration of 100 nM. MS scans were acquired in the positive mode in the mass range 100–2000 m/z and at a resolution set to 120,000. Data analysis was carried out using XCalibur software version 4.1 (Thermo Fisher Scientific).

Wild-type and R273H p53 core domains were de-salted against 20 mM ammonium acetate buffer by using 10 K concentration columns (Vivaspin, GE Healthacare, Chicago, IL). Twenty µM of the purified protein were incubated with 0 µM (control), 50, 100 or 200 µM MQ for 15 min at 21 °C. R175H core domains were de-salted by ZipTip C4 resin tips for MALDI-ToF MS (Merck Millipore, Billerica, MA) following the manufacturer’s protocol. 3.2 µM of R175H protein were treated with 0 µM (control), 10, 25 or 50 µM of MQ for 15 min at 21 °C. 5% formic acid (1:1 volume ratio) was added to the samples to increase the ionization sensitivity. Samples were analyzed by LTQ XL mass spectrometry (Thermo Fisher Scientific, Waltham, MA) fitted with an automated nanospray source (TriVersa Nanomate, Advion Biosciences, Ithaca, NY) using nanoelectrospray chips with spraying nozzels. The ion source was controlled using the Chipsoft 8.3.1 software (Advion Biosciences, Ithaca NY). Three microliters of each sample were loaded into a 96-well plate and injection volume was one and a half microliters. Full scan spectra were collected at the m/z 500–2000 in positive ion mode. The mass spectra of each sample were acquired in profile mode over 4 min. The spectra were analyzed using XCalibur^TM Software (Thermo Fisher Scientific, Waltham, MA). Deconvoluted ESI spectra are presented.

For lipid quantification by shotgun MS, 700 μL of a mixture of internal standards in MTBE/MeOH (5:1.5; [vol/vol]) were added to the dried lipid fractions. MS analyses were performed as previously described (74 (link)) on a Q Exactive instrument (Thermo Fisher Scientific) equipped with a robotic nanoflow ion source TriVersa NanoMate (Advion BioSciences) using nanoelectrospray chips with the diameter of spraying nozzles of 4.1 μm. The ion source was controlled by the Chipsoft 8.3.1 software (Advion BioSciences). Spectra was filtered based on repetition rate as previously described and analyzed by a laboratory-developed script (75 (link), 76 (link)). Lipids were identified by LipidXplorer software (77 (link)).