The extent and effects of peptide sequence scrambling via formation of macrocyclic <Emphasis Type="Italic">b</Emphasis> ions in model proteins |
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Authors: | Irine S Saminathan X Simon Wang Yuzhu Guo Olga Krakovska Sébastien Voisin Alan C Hopkinson K W Michael Siu |
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Institution: | (1) Department of Chemistry, Faculty of Science, Izmir Institute of Technology, 35430 Urla-Izmir, Turkey; |
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Abstract: | The extent and effects of sequence scrambling in peptide ions during tandem mass spectrometry (MS/MS) have been examined using
tryptic peptides from model proteins. Sequencescrambled b ions appeared in about 35% of 43 tryptic peptides examined under MS/MS conditions. In general, these ions had relatively
low abundances with averages of 8% and 16%, depending on the instrumentation used. A few tryptic peptides gave abundant scrambled
b ions in MS/MS. However, peptide and protein identifications under proteomic conditions with Mascot were not affected, even
for these peptides wherein scrambling was prominent. From the 43 tryptic peptides that have been investigated, the conclusion
is that sequence scrambling is unlikely to impact negatively on the accuracy of automated peptide and protein identifications
in proteomics. |
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