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
On Wednesday, January 22, 2014 5:49:36 AM UTC-8, Liang QIAO wrote:
>
> 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
>
>
>
> <https://lh3.googleusercontent.com/-FHaLmbBRsys/Ut_L-wAI0fI/AAAAAAAACfU/sZfM9KY3PYE/s1600/mzxml.JPG>
>
>
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