MALDI‐MS/MS of N‐Terminal TMPP‐Acyl Peptides: A Worthwhile Tool to Decipher Protein N‐Termini

N‐terminal derivatization of proteins with permanently positive charged reagent constitutes a viable mass spectrometry bottom‐up strategy for systematic confident identification of protein N‐termini. Although shotgun nanoLC‐ESI‐MS/MS approaches are commonly applied in that context by dissociating multiply charged molecular ions upon low energy collision‐induced dissociations (CID), we were keen to investigate an alternative sequencing method reckoning on more comprehensive high energy charge remote fragmentations (CRF) available with a MALDI‐Tof/Tof instrument. Hence, two tunable activation methods, i. e. metastable laser‐induced dissociations (LID) and high energy CID, were applied to several synthetic N‐terminal tris(trimethoxyphenyl)phosphonium (TMPP) acetyl peptides and their MS/MS behaviors were compared with low energy CID MS/MS data (LC‐ESI‐QqTof equipment). The amino acid composition was found to play a significant role in the peptide backbone dissociation pathways of these fixed singly charged ions. Proline, arginine, aspartic acid, glutamic acid, but also surprisingly aliphatic residues were impacting the expected sequence fragmentation pattern.