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 On Thursday, January 23, 2014 4:31:53 AM UTC-6, Liang QIAO wrote: > > Dear Hannes, > > Thank you so much for the kind help. > > I will try both methods from you and Jason. > > Best regards > > Liang > > On Wednesday, January 22, 2014 6:29:46 PM UTC+1, Hannes Roest wrote: >> >> 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 >> >> On 22 January 2014 17:03, Jason Winget <[email protected]> wrote: >> > >> > 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 >> >> >> >> >> >> >> > -- >> > You received this message because you are subscribed to the Google >> Groups "spctools-discuss" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> an email to [email protected]. >> > To post to this group, send email to [email protected]. >> > Visit this group at http://groups.google.com/group/spctools-discuss. >> > For more options, visit https://groups.google.com/groups/opt_out. >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
