Proteomics calls for new computational tools. One such tool is the GenomicPeptideFinder (GPF) which aids in intron detection, using mass spectrometric data. While programming GPF and the automation suite AutoMS, a number of tools for the Windows operating system were developed which may be of use in proteomic data analysis.
GenomicPeptideFinder: Mass spectrometric data mining in genomic data bases (Freiburg 10.07)
AutoMS is an automatic pipeline that allows automation of PEAKS, a de novo amino acid sequencing algorithm, Sequest, a database search algorithm, and GPF, the connection in the programs mentioned previously. Raw file extraction and data filtering are also possible.
The GenomicPeptideFinder (GPF)
GPF was first established in 2003 and published in 2004. It has been enhanced ever since. The focus of GPF is to error tolerantly search genomic databases with de novo sequence predictions and to predict introns based on this data.
The DNATranslator is a feature rich software that translates DNA to all or selected reading frames. It works from pasted strings as well as from fasta-files. The translation table is fully customizable.
The QueryCreator creates queries for GPF from DeNovoX, Lutefisk, PEAKS, and Sequest output. It can however be used to filter and transform de novo predictions as well since the output can be adjusted.
The SequestExtractor filters Sequest out-files according to user settable significance thresholds and reports the results in a plain text file which can easily be imported to most databases.
This program simply traverses a fasta-file and reports the number of peptides that fall into a set mass interval. Results are reported in a plain text file containing bins and their peptide count.
This web-based database system allows storage, analysis, and displays of experimental data from, for example, 2 dimensional gel electrophoresis and mass spectrometry. Anything that can be presented as an image can be displayed in this database. Areas e.g. spots on such an image can be selected. The data gained from mass spectrometric analysis of these spots can also be stored (software independent e.g. from Sequest, Mascot, ..). The aim, protein identification, can easily be achieved with this tool. Simply set your thresholds once. Whenever a spot or a gel is accessed, the proteins are detected on the fly. Obviously this version of the database, you see here, is based on the sequence of Chlamydomonas reinhardtii. It displays all published information to anyone, but also contains our current projects, which are however not displayed to the outside. If you have access to a web-server allowing PHP and MySQL, feel free to download our extremely easy installation package.
Jens Allmer, Sebastian Kuhlgert, Michael Hippler (2008)
2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments.
BMC, 9, 302