In-Source Decay and Pseudo-MS³of Peptide and Protein Ions Using Liquid AP-MALDI

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 Abstractᅟ Electronic supplementary materialThe online version of this article (doi:10.1007/s13361-016-1511-0) contains supplementary material, which is available to authorized users.

Collision-induced dissociation of doubly-charged barium-cationized lipids generated from liquid samples by atmospheric pressure matrix-assisted laser desorption/ionization provides structurally diagnostic product ions

“…As doubly charged CID products were observed, it will be possible to perform ETD after CID in the future. CID of SM (d18:1/12:0) revealed a low abundance peak for the sn2 chain (m/z 336.1); [42].…”

The matrix‐assisted laser desorption/ionisation in‐source decay of peptides using ion mobility enabled quadrupole‐time‐of‐flight mass spectrometry

“…To increase the selectivity of an ISD experiment, the first-generation fragments could be fragmented further (pseudo MS 3 experiments). [8][9][10] Matrix interferences could be eliminated using high-resolution mass analysis with Fourier transform ion cyclotron resonance (FTICR) and the subtraction of the matrix signals. This approach has been successfully demonstrated for MALDI imaging.…”

“…MALDI‐ISD thus characterises peptide sequences or protein terminal sequences quickly and sensitively. To increase the selectivity of an ISD experiment, the first‐generation fragments could be fragmented further (pseudo MS 3 experiments) . Matrix interferences could be eliminated using high‐resolution mass analysis with Fourier transform ion cyclotron resonance (FTICR) and the subtraction of the matrix signals.…”

Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey

“…The result is a tandem mass spectrum, which is analyzed using computational methods to identify proteins and their modified variants in the sample. The protein may further be separated and fragmented (MS3) into peptides which may be analyzed to localize modifications to parts of the protein [ 95 ], disambiguate protein identification through sequence tags [ 95 ], improve on confidence score of identifications [ 96 ], help differentiate highly similar proteins [ 97 ], and perform similar targeted (MS n ) analyses [ 98 ], [ 99 ].…”