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Supported MS File Formats

Instruments / Data Formats



e.g. QStar® , QTrap®


Applied Biosystems,
Framingham, MA, USA

e.g. HCT, ultraflexTM, autoflexTM /
XML, ASCII and peaklist files


Bremen, Germany

Mascot Generic Format /
MGF files


Matrix Science,
London, UK

ProteinScapeTM export format


Bruker-Daltonik, Bremen, Germany
Protagen, Dortmund, Germany

e.g. FinniganTM LCQTM Deca XP- / DTA-files

SEQUEST® / XcaliburTM

Thermo Electron,
San Jose, CA, USA


open standard

Institute for Systems Biology,
Seattle, WA, USA

text files

properly formatted; e.g. from MS ExcelTM


compressed peak lists /



For generating MS spectra from WIFF files as they are used in the Analyst software for QStar and other instruments a little tool was developed. More information about the ShowSpectrum-tool can be found here.

Decoy Database Builder
If you want to estimate your false positive protein identification rate with the help of decoy databases then build them with the DDBB. Reverse, shuffle or random decoy databases from FASTA files or single protein sequences. Supporting NCBI, IPI and UniprotKB protein databases.

Find Pairs
Universal software for easy quantitation of stable isotope labeling experiments. 14N/15N, ICAT, SILAC, ICPL, iTRAQ and other labeling techniques are supported. Filtering of spectral noise and outlier detection lead to accurate and fast results.

Software for comparing large sets of protein lists. This is useful if you want to find out which proteins are common or unique between different experiments. Supports union, intersection, difference and symmetric difference of up to three different lists; counts the common entries of up to 38 protein lists and counts the occurrence of all elements in a single list. The software is tailor-made for protein lists, but every other text list can be used if each entry is in a single line.


The software is platform independent and thus works on every Java capable computer directly from this website.