In-Source Decay and Pseudo-MS(3) of Peptide and Protein Ions Using Liquid AP-MALDI

Atmospheric pressure MALDI on a Q-Exactive instrument was optimized for in-source decay and pseudo-MS(3). The dependence of AP-MALDI ISD on the MALDI liquid matrix was investigated for peptides and proteins. The liquid matrices enabled long-life ISD signal, and exhibited high fragment ion yield and signal stability. Extensive a-, b-, c-, y-, and z-type fragment series were observed depending on the matrix used but were most extensive with 2,5-DHB. Complete sequence coverage of small peptide and intact protein-terminus sequence tags were obtained and confirmed using HCD as a pseudo-MS(3) method. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13361-016-1511-0) contains supplementary material, which is available to authorized users.