Quantitative MALDI-TOF and LA-LDI MS Analysis

Matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry (MALDI-TOF MS) was performed using a Bruker UltrafleXtreme or Ultraflex III spectrometer equipped with a 355 nm Nd:YAG laser (Smartbeam 1000 or 200 MHz), with α-cyano-4-hydroxycinnamic acid (α-CHCA) or sinapinic acid as matrices^{22 (link)}. Label-assisted laser desorption/ionization mass spectrometry (LA-LDI MS) was performed using a Bruker UltrafleXtreme spectrometer as for MALDI-TOF MS without matrices^{25 (link)}. Samples dissolved in 50% aq. MeOH or MeCN / 0.1–1% TFA were spotted on an MTP384 ground steel target plate and air-dried according to the manufacturer’s instructions. To determine the detectable sensitivity of the molecular ion peaks of dmpy–OMe (1) and apy–OMe (2) on LA-LDI MS, standard parameters for the reflector positive mode of MALDI MS were used with 20% laser intensity (Fig. 1b,c). For the LA-LDI MS and MS/MS analyses of dmpy-labeled peptides (Figs. 2 and S2), standard parameters for the reflector positive mode of MALDI MS were used except for detector gain voltage (changed from 1650 to 1860 V). Tandem MALDI MS/MS analysis was performed using a Bruker UltrafleXtreme spectrometer (Fig. S6).