Publications - Published papers
Please find below publications of our group. Currently, we list 565 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (
) is restricted to our local network and chosen collaborators.
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) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.
Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics
Stephan A. Müller, Sven Findeiß, Sandy R. Pernitzsch, Dirk K. Wissenbach, Peter F. Stadler, Ivo L. Hofacker, Martin von Bergen, Stefan Kalkhof
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Status: Published
Journal of Proteomics 86:27-42 (2013)
Abstract
Correct annotation of protein coding genes is the basis of conventional data analysis in
proteomic studies. Nevertheless, most protein sequence databases almost exclusively rely on
gene finding software and inevitably also miss protein annotations or possess errors.
Proteogenomics tries to overcome these issues by matching MS data directly against a
genome sequence database. Here we report an in-depth proteogenomics study of Helicobacter
pylori strain 26695. MS data was searched against a combined database of the NCBI
annotations and a six-frame translation of the genome. Database searches with Mascot and
X!Tandem revealed 1115 proteins identified by at least two peptides with a peptide false
discovery rate below 1%. This represents 71% of the predicted proteome. So far this is the
most extensive proteome study of H. pylori. Our proteogenomics approach unambiguously
identified four previously missed annotations and furthermore allowed us to correct sequences
of six annotated proteins. Since secreted proteins are often involved in pathogenic processes
we further investigated signal peptidase cleavage sites. By applying a database search that
accommodates the identification of semi-specific cleaved peptides, 63 previously unknown
signal peptides were detected. The motif LXA showed to be the predominant recognition
sequence for signal peptidases.
Keywords
Proteogenomics Proteomics Coding sequence Helicobacter pylori Signal peptide