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Title (Primary) Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics
Author Müller, S.A.; Findeiß, S.; Pernitzsch, S.R.; Wissenbach, D.K.; Stadler, P.F.; Hofacker, I.L.; von Bergen, M.; Kalkhof, S.;
Journal Journal of Proteomics
Year 2013
Department METABOX; PROTEOM;
Volume 86
Language englisch;
POF III (all) F11;
Keywords Proteogenomics; Proteomics; Coding sequence; Helicobacter pylori; Signal peptide
UFZ wide themes RU3;
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 proteogenomic 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.
ID 13718
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=13718
Müller, S.A., Findeiß, S., Pernitzsch, S.R., Wissenbach, D.K., Stadler, P.F., Hofacker, I.L., von Bergen, M., Kalkhof, S. (2013):
Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics
J. Proteomics 86 , 27 - 42