In-Source Decay and Pseudo-MS3 of Peptide and Protein Ions Using Liquid AP-MALDI

J Am Soc Mass Spectrom. 2016 Dec;27(12):2075-2079. doi: 10.1007/s13361-016-1511-0. Epub 2016 Oct 17.


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 Abstract ᅟ.

Keywords: In-source decay; MALDI; MS/MS; Pseudo MS3; T3 sequencing.

MeSH terms

  • Amino Acid Sequence
  • Ions
  • Peptides / analysis*
  • Peptides / chemistry
  • Proteins / analysis*
  • Proteins / chemistry
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization*


  • Ions
  • Peptides
  • Proteins