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Volume 18 (2004), Issue 3, Pages 441-451

Skimmer CID‒ion trap mass spectrometry of phosphotyrosine‒containing peptides

Melissa D. Zolodz1 and Karl V. Wood2

1Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Dr., RHPH Bldg, West Lafayette, IN 47907, USA
2Department of Chemistry, Purdue University, 575 Stadium Mall Dr., RHPH Bldg, West Lafayette, IN 47907, USA

Copyright © 2004 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Proteomic analysis is becoming a popular field in science. Analysis of protein modifications is useful in deciphering cellular functions and errors in pathways that can result in disease. There has been increased interest in the phosphotyrosine proteome. Due to the difficulty in finding the location of the tyrosine phosphorylation site in the tyrosine phosphorylated peptide or even to verify that the parent protein is a phosphotyrosyl‒protein, new analytical tools are being developed. The phosphotyrosine immonium ion can be produced via skimmer CID for detection via ion trap mass spectrometry and is a useful marker for the indication of the presence of a phosphotyrosine residue. Skimmer CID analysis can also be used to differentiate phosphotyrosine‒containing peptides from other phosphorylated peptides. In this study, phosphotyrosine‒containing peptides were analyzed by skimmer CID in an ion trap mass spectrometer. The factors affecting the signal abundance of the phosphotyrosine immonium ion were investigated.