How to extract the intensities for peaks with a specific m/z from the mzxml file

[Liang QIAO]

Hi All,

I want to get the intensities of peaks with a specific m/z at different retention times from hundreds of thermo RAW files. 

I have converted a RAW file into a mzxml file, and opened the mzxml file by excel to display the xml table.

In the table, I found only the lowMz for the peak with lowest m/z, the highMz for the one with highest m/z and the basePeakMz for the most intensive one.

However, there should be hundreds of peaks according to the peaksCount

I put here a figure to show the displayed xml table by excel.

Is there a way to display all the counted peaks with m/z as well as the corresponding intensities at each retention time?

Thank you very much for your help.

Best wishes

Liang 

[Jason Winget]

Hi Liang, this is something I've been working on recently. The peak intensities are compressed, so you need to decompress them to generate a table of peaks and intensities.

You will almost certainly want to do this with a script instead of in Excel.

For mzXML files, I first extract all scan events, then parse the peaks element as follows (in python, using the base64, struct, and lxml modules):

----

line = elem.xpath('mzXML:peaks', namespaces=NS)[0].text

decoded = base64.standard_b64decode(line)

tmp_size = len(decoded) / 8

unpack_format = "!%dd" % tmp_size # This is important. The data is double-double encoded

idx = 0

mz_list = []

intensity_list = []

for val in struct.unpack_from(unpack_format, decoded):

    if(idx%2 == 0):

        mz_list.append(float(val))

    else:

        itensity_list.append(float(val))

    idx += 1

----

This returns two lists containing the m/z values and intensities, respectively for each scan.

For mzML, I've found it easier to use the pymzml module for python. Here is some code to get you started with that:

----

msrun = pymzml.run.Reader(filepath)

for s in msrun:

    if s['id'] in scans:

        for mz, i in s.peaks:

            print(mz, i)

----

Hope this gets you going.

Best,

Jason

[Hannes Röst]

Hi Liang

For easy handling of mzXML, you can also use pyopenms

import pyopenms
exp = pyopenms.MSExperiment()
pyopenms.FileHandler().loadExperiment(filepath, exp)
for spectrum in exp:
for peak in spectrum:
print peak.getMZ(), peak.getIntensity()

It is based on the OpenMS package and is available through PyPI:
https://pypi.python.org/pypi/pyopenms

I hope this helps

Hannes

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[Jason Winget]

Hannes:

I wish I had found pyopenms when I was trying to solve this! The unpacking of the peak/intensity values was not trivial to sort out

Time to refactor my code...

[Hannes Röst]

Hi Jason

We just completed the final release last August and published the
paper these days, so pyOpenMS has not been around that long. I hope it
is useful and stays useful to the community. If you have comments or
suggestions, please just send me an email :-)

Hannes

[Liang QIAO]

Dear Jason,

Thank you very much for the help.

I will try with your method.

Best regards

Liang

[Liang QIAO]

Dear Hannes,

Thank you so much for the kind help.

I will try both methods from you and Jason.

Best regards

Liang

[Taejoon Kwon]

The other option would be using ProteoWizard, concerting your RAW files (or mzXML files) to ms1 and ms2 format. I think you can intuitively interpret those text. Or see the following paper http://www.ncbi.nlm.nih.gov/pubmed/15317041

Taejoon