Error Using mzxml read

Hello:

I am using MATLAB 2015a.

I converted a set of Thermo.raw files into mzXML using msconvert.gui (Proteowizard). The files are from an Thermo Orbitrap Velos, and contain MS2 data.

I am trying to read them into MATLAB using mzxmlread.m and I am getting the following error

>> testscript
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;

Error in testscript (line 1)
mzXMLStruct = mzxmlread('SampleA_Search1.mzXML');

I have seen this question two other times on MATLAB central- I commented on those as well, but none have been answered. any feedback would be really appreciated.

Thank you

Katie

[Yuqing Ye]

Hi,

I have the same question with you. If you have solved this, would you please tell me the solution?

Thank you

Yuqing Ye

Answer 1

[Yuqing Ye]

Hi,

I have solved it!

When using msconvert you should choose these options as the picture below shows.

-Yuqing Ye

[天琪 李]

THANKS!

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 Katie,

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.

Answer 4

[Jingxuan Li]

Hi Yuqing et al, I followed your instruction in generating the file. However, I got error as attached---may I ask if you have seen this before, and how did you deal with it? Thanks!

Jay