Abstract
Atmospheric pressure MALDI on a Q-Exactive instrument was optimized for in-source decay and pseudo-MS3. 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-MS3 method. Graphical ᅟ Electronic supplementary materialThe online version of this article (doi:10.1007/s13361-016-1511-0) contains supplementary material, which is available to authorized users.
Highlights
I n-source decay (ISD) is the principal MS/MS method available to matrix-assisted laser desorption/ionization (MALDI) that can be applied to intact proteins
This is pertinent because the generation of ISD fragments and the sequence coverage obtained are highly influenced by the MALDI matrix and laser fluence [19,20,21,22,23]
This study demonstrated the clear advantage of using liquid matrix sample preparations for AP-MALDI ISD and AP-MALDI pseudo-MS3 for the characterization of peptides and proteins
Summary
I n-source decay (ISD) is the principal MS/MS method available to matrix-assisted laser desorption/ionization (MALDI) that can be applied to intact proteins. We investigated the analytical capability of AP-MALDI using long-life matrices to generate ISD and pseudo-MS3 fragments of peptides and proteins. The experiments were performed on a Q-Exactive Plus equipped with an AP-MALDI imaging source, which enabled accurate mass, high mass resolution characterization of the ISD, and pseudo-MS3 fragments.
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