massWolf: deisotoping and cetroiding

[Joo]

I have a Q-TOF dataset
I converted .RAW files to mzXML using massWolf_2006Nov06
I got mzXML but it does not contains charge state, and the peaks do
not seem to be cetroided peaks,,,
I need deisotoped, centroided peak list
Is there any option that does deisotoping and centroiding in massWolf?
if not, is there any other software that could convert Q-Tof .RAW file
to mzXML file
I need help~

[Matthew Chambers]

Unfortunately, charge state information is not available in the RAW data, so charge state would be a post-processing step. There is also no vendor-provided
peak picking, so any centroiding has to be post-processing as well. Waters's best solution for this is the not-free ProteinLynx Global Server (PLGS) which does
both charge state determination and centroiding. MassLynx itself can do some denoising and peak picking, but not charge state inference IIRC.

There may be some good post-processing tools for inferring charge state and centroiding out there, but I'm not aware of ones that that both do a good job AND
read mz[X]ML AND write mz[X]ML. Perhaps someone else can clue me in on that.

-Matt

[Alex_PCB]

I believe you could use OpenMS to post-process your mzML files.
cheers,
alex

On Jul 14, 7:49 pm, Matthew Chambers <matt.chamber...@gmail.com>
wrote:

[Gautam Saxena]

Does msconvert do deisotoping of isotopic clusters and charge-deconvolution, as described in the webpage on "ms2 spectrum processor": http://ms.imp.ac.at/?goto=ms2spectrumprocessor

If not, is there any recommended open-source solution for this? The best I could find so far is this publication by Pavel Pezner which does describe 1 free (not sure if it's open source) solution: http://www.mcponline.org/content/9/12/2772.full.pdf