How to fix an mzxmlread error?

I used the program msconvert from proteowizard to convert my Thermo .raw files to .mzXML files. When I use the mzxmlread command in MATLAB2015b(mzxmlread('data1.mzXML');) in matlab, I get this...

Starting to parse document...

Building mzXML substructure...

Building scan substructure...

Error using typecast

The first input must contain a multiple of 8 elements to convert from int8 (8 bits) to double (64 bits).

Error in mzxmlread>processPeaks (line 699) mzpeaks = swapbytes(typecast(peaks,'double'));

Error in mzxmlread/parseScan (line 555) out.(elementNameScan)(countScan+1).peaks.mz = processPeaks(b64.decode(data),64);

Error in mzxmlread (line 420) parseScan;

[cccc17]

I have the same error. Do you have any solution?

[Katie]

I HAVE THIS ERROR AS WELL.

Anybody? Please?

Answer 1

[Kundai Sachikonye]

I had the same problem for a while and stumbled upon a solution. When using MSConvert to convert raw files to mzXML files, set binary precision to 32bit and add "Write index" and "TPP Compatability" as options and ensure that "Use zlib compression" tab is unchecked. Finally, for the filter section, add "Pick Peaking", check "Prefer Vendor" tab and add the appropiate MS Levels you require. After the relatively quick conversion, your file should load into MATLAB without any errors.

[Anyin Li]

This solved the similar problem I am having

Answer 2

[Arthur Goldsipe]

Hi,

I believe the mzXML file is invalid. mzxmlread could give a more helpful error message, but the error occurs when the peaks data for a run is invalid. Perhaps msconvert did not correctly encode the data.

-Arthur

Answer 3

[Luuk van Oosten]

Dear Shenae, Katie, cccc17,

The problem might occur due to the fact that your mzXML file is improperly generated, as Arthur Goldspie already remarked.

Note that MATLAB is only able to handle mzXML files that are conform the 2.1 specifications or earlier. Try to generate your mzXML file with an older version and try again... I believe that you can find those versions somewhere over here.

That might solve it.