A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment
- Author(s)
- Wolfgang Höhenwarter, Joost T. van Dongen, Stefanie Wienkoop, Mtthias Steinfath, Jan Hummel, Alexander Erban, Ronan Sulpice, Babette Regierer, Joachim Kopka, Peter Geigenberger, Wolfram Weckwerth
- Abstract
The dynamics of a proteome can only be addressed with large-scale, high-throughput methods. To
cope with the inherent complexity, techniques based on targeted quantification using proteotypic
peptides are arising. This is an essential systems biology approach; however, for the exploratory discovery
of unexpectedmarkers, nontargeted detection of proteins, and proteinmodifications is indispensable.
We present a rapid label-free shotgun proteomics approach that extracts relevant phenotype-
specific peptide product ion spectra in an automated workflow without prior identification.
These product ion spectra are subsequently sequenced with database search and de novo prediction
algorithms. We analyzed six potato tuber cultivars grown on three plots of two geographically separated
fields in Germany. For data mining about 1.5 million spectra from 107 analyses were aligned
and statistically examined in approximately 1 day. Several cultivar-specific protein markers were
detected. Based on de novo-sequencing a dominant protein polymorphism not detectable in the
available EST-databases was assigned exclusively to a specific potato cultivar. The approach is applicable
to organisms with unsequenced or incomplete genomes and to the automated extraction of
relevantmass spectra that potentially cannot be identified by genome/EST-based search algorithms.
- Organisation(s)
- External organisation(s)
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Universität Potsdam
- Journal
- Proteomics
- Volume
- 8
- Pages
- 4214-4225
- No. of pages
- 12
- ISSN
- 1615-9853
- Publication date
- 2008
- Peer reviewed
- Yes
- Austrian Fields of Science 2012
- 106002 Biochemistry, 1030 Physics, Astronomy, 106037 Proteomics, 106031 Plant physiology
- Portal url
- https://ucris.univie.ac.at/portal/en/publications/a-rapid-approach-for-phenotypescreening-and-database-independent-detection-of-csnpprotein-polymorphism-using-mass-accuracy-precursor-alignment(6701fa06-5bc8-44bc-ad8f-1f2bddd8ce42).html