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. Author manuscript; available in PMC: 2012 Nov 15.
Published in final edited form as: Amino Acids. 2012 Jul 22;43(3):1049–1060. doi: 10.1007/s00726-012-1286-y

Table 1.

Strategy for identifying amino acid residues modified by ubiquitin and Ubls. The conjugated proteins are usually digested by trypsin to generate a specific tag (e.g., GG for ubiquitin) on the modified residues, resulting in a mass shift that is detectable during MS and MS/MS scans. The mass of human Fat10 tag may change because of natural variations in sequence (UniProtKB/Swiss-Prot O15205).

Human Ub or UBL Remnant on modified peptides after trypsin digestion Mass change in MS and MS/MS Problems Solutions
Ub graphic file with name nihms408247t1.jpg Monoisotopic mass shift of 114.0429 Da in MS and MS/MS Ub, Nedd8, and ISG15 modifications lead to the same mass change after trypsin digestion Pre-enrichment of modified proteins prior totrypsin digestion
Nedd8 graphic file with name nihms408247t2.jpg
ISG15 graphic file with name nihms408247t3.jpg
SUMO-1 graphic file with name nihms408247t4.jpg Large mass shift in MS and complex production patterns in MS/MS Weak signal in MS and complex MS/MS spectra that are difficult to interpret

  1. Software tool (e.g. SUMmOn)

  2. UBL spectral library

  3. Engineering tryptic sites at the C-terminus by mutagenesis
SUMO-2/3 graphic file with name nihms408247t5.jpg
Fat10 graphic file with name nihms408247t6.jpg