Abstract

High sensitivity and low detection limits are two characteristics that have made mass spectrometry (MS) a very useful analytical method; for example, atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) can detect peptides in a protein digest at the femtomole level. MS has found wide usage in the field of proteomics primarily for the identification of components of unknown mixtures and the determination of post-translational modifications in proteins. A relatively new ionization method, AP-MALDI is gaining popularity compared to conventional vacuum MALDI as it is a softer ionization technique, operates at atmospheric pressure and is decoupled from the mass analyzer. MALDI uses an UV laser to irradiate samples consisting of co-crystallized matrix and analyte. Studies have identified -cyano-4-hydroxycinnamic acid (HCCA) and 2,5-dihydroxybenzoic acid (DHB) as the leading matrixes of choice. In this study, the matrix analyte ratio was optimized for the identification of single and multiple peptides using a Bruker Esquire quadrupole ion trap mass spectrometer. The mentioned matrixes along with different analyte to matrix ratios were compared using the peptides: VGVRVR, AAAAR, GVAYFMVHPD, DRVYIHPF (Angiotensin II) RPPGFSPFR (Bradykinin) and RPPGFSPF (Des-Arg9Bradykinin). DHB was the matrix of choice because it formed more crystals and therefore increased the likelihood of obtaining a signal with high intensity. A 1:20000 analyte to matrix ratio gave the best signal on average for the peptides. In general, the more concentrated the matrix solution, the better the crystals formed.