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Yasser A. Elnakady

Assistant Professor

Assistant Prof.

كلية العلوم
Building 5, Room AB 70
المنشورات
مقال فى مجلة
2009

De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation

, By:Bertsch, A ; Leinenbach, A ; Pervukhin, A ; Lubeck, M ; Hartmer, R ; Baessmann, C ; Elnakady, YA . 2009

Abstract

De novo sequencing of peptides using tandem MS is difficult due to missing fragment ions in the spectra commonly obtained after CID of peptide precursor ions. Complementing CID spectra with spectra obtained in an ion-trap mass spectrometer upon electron transfer dissociation (ETD) significantly increases the sequence coverage with diagnostic ions. in the de novo sequencing algorithm CompNovo presented here, a divide-and-conquer approach was combined with an efficient mass decomposition algorithm to exploit the complementary information contained in CID and ETD spectra. After optimizing the parameters for the algorithm on a well-defined training data set obtained for peptides from nine known proteins, the CompNovo algorithm was applied to the de novo sequencing of peptides derived from a whole protein extract of Sorangium cellulosum bacteria. To 2406 pairs of CID and ETD spectra contained in this data set, 675 fully correct sequences were assigned, which represent a success rate of 28.1%. It is shown that the CompNovo algorithm yields significantly improved sequencing accuracy as compared with published approaches using only CID spectra or combined CID and ETD spectra

Keywords

رقم المجلد
30
رقم الانشاء
21
مجلة/صحيفة
ELECTROPHORESIS
الصفحات
3736-3747
مزيد من المنشورات