Sequence Scrambling in Shotgun Proteomics is Negligible

Analysis of 15,897 low-energy (CAD) and 10,878 higher-energy (HCD) collisional dissociation mass spectra of doubly protonated tryptic peptides taken with high resolution revealed that the rate of sequence scrambling due to b-ion cyclization is negligible (<1%) and can be safely ignored as a possi...

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Bibliographic Details
Published inJournal of the American Society for Mass Spectrometry Vol. 22; no. 7; pp. 1121 - 1124
Main Authors Goloborodko, Anton A., Gorshkov, Mikhail V., Good, David M., Zubarev, Roman A.
Format Journal Article
LanguageEnglish
Published New York Springer-Verlag 01.07.2011
Springer Nature B.V
Subjects
Analytical Chemistry
Bioinformatics
Biotechnology
Chemistry
Chemistry and Materials Science
Databases, Protein
Energy of dissociation
Fragments
Mass spectra
Mass spectrometry
Medicin och hälsovetenskap
Organic Chemistry
Peptide Fragments - chemistry
Peptide Mapping - methods
Peptides
Proteomics
Proteomics - methods
Search engines
Short Communication
Tandem Mass Spectrometry - methods
HCD
Peptide fragmentation
De novo sequencing
Database search
CAD
Proteomics
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Summary:Analysis of 15,897 low-energy (CAD) and 10,878 higher-energy (HCD) collisional dissociation mass spectra of doubly protonated tryptic peptides taken with high resolution revealed that the rate of sequence scrambling due to b-ion cyclization is negligible (<1%) and can be safely ignored as a possible source of erroneous sequence assignment in shotgun proteomics. On the other hand, there is significant presence of normal (non-scrambled) internal fragments in HCD, which should be taken into account by MS/MS search engines.
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ISSN:1044-0305
1879-1123
1879-1123
DOI:10.1007/s13361-011-0130-z