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Leveraging Immonium Ions for Targeting Acyl‐Lysine Modifications in Proteomic Datasets
Author(s) -
Muroski John M.,
Fu Janine Y.,
Nguyen Hong Hanh,
Ogorzalek Loo Rachel R.,
Loo Joseph A.
Publication year - 2021
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.202000111
Subject(s) - lysine , chemistry , ion , mass spectrometry , tandem mass spectrometry , shotgun , computational biology , combinatorial chemistry , biochemistry , biology , amino acid , chromatography , gene , organic chemistry
Acyl modifications vary greatly in terms of elemental composition and site of protein modification. Developing methods to identify acyl modifications more confidently can help to assess the scope of these modifications in large proteomic datasets. The utility of acyl‐lysine immonium ions is analyzed for identifying the modifications in proteomic datasets. It is demonstrated that the cyclized immonium ion is a strong indicator of acyl‐lysine presence when its rank or relative abundance compared to other ions within a spectrum is considered. Utilizing a stepped collision energy method in a shotgun experiment highlights the immonium ion. By implementing an analysis that accounted for features within each MS 2 spectrum, the method clearly identifies peptides with short chain acyl‐lysine modifications from complex lysates. Immonium ions can also be used to validate novel acyl modifications; in this study, the first examples of 3‐hydroxylpimelyl‐lysine modifications are reported and they are validated using immonium ions. Overall these results solidify the use of the immonium ion as a marker for acyl‐lysine modifications in complex proteomic datasets.