Dear reader,
My data aquired by the mass spectrometer (in *.raw format), is converted by some program (called ReAdW, available there) to make a *.mzXML file. I've been importing these mzXML files into MATLAB for some time now using the bioinformatics toolbox. What I do is the following:
mzxml_struct = mzxmlread('mydatafile.mzxml');
That has yielded me a few hundred mzxml_structs in MATLAB on which I could calculate a lot. Used this for months, even used different methods and settings on the mass spectrometer and it never failed (both ReAdW and MATLAB). But today MATLAB did not work anymore. I must admit that I used some other settings on the mass spectrometer, but since I changed settings before I don't think the problem lies there. I got the following:
Error using mzxmlread/parseScan (line 551)Java exception occurred:java.lang.ArrayIndexOutOfBoundsException: -1 at org.apache.commons.codec.binary.Base64.isBase64(Base64.java:137) at org.apache.commons.codec.binary.Base64.discardNonBase64(Base64.java:478) at org.apache.commons.codec.binary.Base64.decodeBase64(Base64.java:374) at org.apache.commons.codec.binary.Base64.decode(Base64.java:220)Error in mzxmlread (line 420) parseScan;Error in my_mzXML_script (line 14)mzxml_struct = mzxmlread('mydatafile.mzxml');
I do understand that somewhere Matlab is trying to access a certain array, but that that array does not exist or that that array contains stuff that does not belong there which it cannot use in the mzxmlread('data.mzxml') function. However, I am not able to solve this problem.
Some stuff I tried, but did not work
-turning it off and on again
-allocate more heap space to Java
-update Java
-checked if my version of the ReAdW program was old enough for MATLAB (it was)
– Unplug my external monitor from my laptop
– Use previously aquired data and run the script; this still works
I'm currently using the following version of MATLAB (if it is any help to you):
MATLAB Version: 8.3.0.532 (R2014a)MATLAB License Number: my licence numberOperating System: Microsoft Windows 8 Version 6.2 (Build 9200)Java Version: Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
With all the fancy extra toolboxes you can think of.
If you have any idea how to solve this problem, I would be very grateful.
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