Documentation

more will be available soon ...

In the meantime you may take a look at the change log or the publications where many questions are answered.

Supported MS File Formats

Instruments / Data Formats	Software	Company
e.g. QStar^® , QTrap^®	Analyst^®	Applied Biosystems, Framingham, MA, USA
e.g. HCT, ultraflex^TM, autoflex^TM / XML, ASCII and peaklist files	XMASS^TM	Bruker-Daltonik, Bremen, Germany
Mascot Generic Format / MGF files	Mascot^TM	Matrix Science, London, UK
ProteinScape^TM export format	ProteinScape^TM	Bruker-Daltonik, Bremen, Germany Protagen, Dortmund, Germany
e.g. FinniganTM LCQ^TM Deca XP- / DTA-files	SEQUEST^® / Xcalibur^TM	Thermo Electron, San Jose, CA, USA
mzXML	open standard	Institute for Systems Biology, Seattle, WA, USA
text files	properly formatted; e.g. from MS Excel^TM	n.a.
compressed peak lists / CPL-files	Peakardt	n.a.

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.

Here is an introduction to the use of the Decoy Database Builder.

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.

If you are interested in protein quantitation with Peakardt.FindPairs please read the short introduction to the FindPairs - module (in german: FindPairs).
Find here a Peakardt properties file for use with ICPL-labeling when doing automatic quantitation with the FindPairs algorithm on an ABI QSTAR mass spec instrument.
Here is the properties file used for ¹⁵N-labeling measured on a QSTAR instrument.
A short introduction in getting peaklists from the QSTAR with the Analyst software (in german). It is shown how to convert RAW files from LC/MS runs to importable peaklists.

SetOperations
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.

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

If the software is not starting correctly, this will most likely be caused by the Java installation on your PC. Make sure that the latest Java version is installed (at least version 1.5 of the JRE). Get it here. The next step is that the JNLP and JAR files are correctly connected to the appropriate applications in your web browser (javaws or java).
To use the software without a connection to the internet, start the Java webstart software installed on your computer and choose the appropriate application from the java cache. The webstart software , javaws.exe usually resides in your java/bin folder, where java is the Java software installation folder.

If you have any further questions, do not hesitate to send me an email: kai.reidegeld@rub.de