1 Topic by luismsanchez

  • luismsanchez
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Topic: Peak Picking crashes with some data files in mMass 5

Hi,
I have data from a MALDI-ToF model Voyager DE STR. I export them to ASCII files, or convert them to compressed mzXML, non-compressed mzXML, or mzDATA using PyMsXML 0.5.4 under Windows 7 and Python 2.7.3 (PyMsXML seems to work under Python 3.2.3, too).

I process my data files using the defaults for MALDI-ToF peptides (except cropping range). mMass can open my datafiles, crop them, apply baseline correction, and smooth them. However, with some data files, it crashes during the "Peak picking" step. Those troublesome input files worked fine with an older version of mMass, which was probably version 3 (I am not sure).

I have tried the last versions of mMass in Windows 7, Windows XP, and Debian Linux (Lubuntu 12.04)... to no avail. The format of the data file does not matter, either. If it is going to crash, it crashes with mzXML, mzDATA, or ASCII. However, when I tried the ASCII format I also got a log file stating:
--------------------
Exception in thread Thread-10:
Traceback (most recent call last):
  File "threading.pyo", line 552, in __bootstrap_inner
  File "threading.pyo", line 505, in run
  File "gui\panel_processing.pyo", line 1828, in runApplyPeakpicking
  File "mspy\obj_scan.pyo", line 545, in labelscan
  File "mspy\mod_peakpicking.pyo", line 235, in labelscan
MemoryError

Unhandled exception in thread started by <bound method Thread.__bootstrap of <Thread(Thread-4, stopped 6284)>>
--------------------

I no longer have my old version of mMass. Is it available for download? Should I post another message with an ASCII spectra? It takes 477 KB, but I do no see how to attach the compressed mzXML version (176 KB).

Best regards, and congratulations for a great program.

2 Reply by Martin

  • Martin
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Re: Peak Picking crashes with some data files in mMass 5

Hi,
to download any old version just go to the website and choose the one you like.

[url]http://www.mmass.org/download/old.php[/url]

In your report, there is some memory error mentioned so it might be a problem of insufficient ram. Anyway, you can send me the file and detailed processing settings and I can try it. (use support at mmass.org)

3 Reply by Martin

  • Martin
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Re: Peak Picking crashes with some data files in mMass 5

Hi Luis,
thanks for the data. It helps me a lot! It takes really long time to figure out what's wrong but now it is fixed. Please wait for a new version, which will be released soon.

Martin