mzXML peak detection (deisotoping) software

[myaxelb]

Dear all,

I have mzXML raw MS files from a MALDI TOF MS (ABI 4700) and urgentlty need a nice software or JAVA code to find monoisotopic peaks in each spectrum! I prefer JAVA because I am able to read that code.
I tried Decon2LS, Mascot Distiller and the Algo implemented in the ABI Data Explorer Software. All these algotithms have problems in finding the correct peaks and often fail with overlapping isotope patters.
We use a quadruplex isotope labeling strategy (on protein level).Getting the mzXML raw file, I want to calculate the deisotoped peaklist (monoisotopic mass and isotopic cluster area) out of that to search for the typical mass pattern of 4 peaks (quadruplets). Later I need to quantify each quadruplet.

Can anybody help me?
Since I am a computer scientist I would prefer program code because with taht I can clearly see how the algorithm really works....

Please send answers to:[Only registered users see links. ].de
Best regards!!

[shannon_t]

Have you tried Hardklör :
proteome.gs.washington.edu/software/hardklor/documentation.html