Software

We are establishing bioinformatics tools that are aimed to facilitate mass spectrometric analyses of prokaryotic as well as for eukaryotic organisms with complex gene structures. Here we are aiming to use mass spectrometric data for genomic data mining and annotation of protein-coding genes. We devised an algorithm, the GenomicPeptideFinder (GPF), which takes advantage of de novo amino acid predictions of MS/MS data enabling detection of intron-split and/or alternatively spliced peptides when deduced from genomic DNA (Allmer et al., 2004, Allmer et al., 2006, Specht et al.,2011a). Further, we generated a platform for proteomic analysis (Specht et al. 2011b), and we devised different algorithms aimed for improved mass spectrometric data mining, including quantitative analyses using qTRACE (Terashima et al., 2010,) and pyQms (Leufken et al., 2017), we developed a fast parser for mzML data (Bald et al., 2011, Kosters et al., 2018) and established a python-based tool named “SugarPy” for de novo identification of N-glycosylated peptides and their N-glycan compositions from bacteria to human (Esquivel et al., 2016, Schulze et al., 2017, 2018, Oltmanns 2020, Schulze et al., 2020). With Crosslinx, we also devised a tool for the analysis of crosslinked peptides via mass spectrometry (Ozawa et al., 2018).


For proteomic analyses the laboratory is equipped with a hybrid linear ion-trap mass spectrometer (Q-Exactive plus-Orbitrap, Thermo Fischer) that is coupled to an Ultimate Nano liquid chromatography system.

 

 

 

 

Proteomics Podcast (10.11.06)

 

 

 

Workshop :

GenomicPeptideFinder: Mass spectrometric data mining in genomic data bases (Freiburg 10.07)
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  • Obsolete

    AutoMS

    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.
    AutoMS

    The DNATranslator

    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

    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

    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.

    PepDist

    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.

    2DB (WWUPepProtDB)
    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.
    2DB

    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