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J Am Soc Mass Spectrom. 2007 Jan;18(1):57-63. Epub 2006 Sep 28.

How to discriminate between leucine and isoleucine by low energy ESI-TRAP MSn.

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Department of Experimental Medicine-Biochemistry Section and Center of Excellence for Biomedical Research (DIMES), University of Genoa, Genoa, Italy.


In peptide sequencing experiments involving a single step tandem mass acquisition, leucine and isoleucine are indistinguishable because both are characterized by a 113 Da mass difference from the other peptide fragments in the MS2 spectrum. In this work, we propose a new method to distinguish between these two amino acids in consecutive MSn experiments, exploiting a gas-phase fragmentation of isoleucine that leads to a diagnostic 69 Da ion. We used this method to assess the Leu/Ile residues of several synthetic peptides. The procedure was then tested on a tryptic digest of myoglobin, assigning the correct amino acid in the majority of the peptides. This work was performed with an old and low-resolution instrument, thus demonstrating that our method is suitable for a wide number of ion trap mass spectrometers, not necessarily expensive or up-to-date.

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