Hi RawProt, all these formats just encode the data recorded from the instrument, either in profile mode or as peaks. The peaks are recorded as m/z and intensity values. One can convert m/z to the mass if you know the charge (z), usually just 1,2,3,4. It's not just straight division since you have to account for proton mass and other stuff, but close. But every peptide has a series of peaks due to different isotopes. One can guess which is the monoisotopic peak, but this is sometimes difficult and error prone, depending on the instrument. So mzML and wiff just encode the peaks that were seen in m/z units. That's all you'll find. pepXML, on the other hand, encodes the (presumed, but not necessarily correct) monoisotopic mass.
The situation is a bit complex, so there's no easy answer to your question. Regards, Eric > -----Original Message----- > From: [email protected] [mailto:spctools- > [email protected]] On Behalf Of RawProt > Sent: Thursday, September 22, 2011 2:34 AM > To: spctools-discuss > Subject: [spctools-discuss] Monoisotopic mass in mzML > > I am designing database of different file formats exited in proteomics > (mzML, > wiff, pepXML). My target is finding monoisotopic mass from different > files under different run/scan > with meta-data and store them in the database. > > I have gone through the documentation of mzML but couldn't really find > term > monoisotopic mass, different term have been used in mzML which I am > pretty > sure. I am went through different mzML samples and try to understand > the > element hierarchy. So what term denotes monoisotopic mass weight in > mzML? > > Element <run> -> <spectrumList> -> <spectrum> -> <precursorList> -> > <selectedIonList> -> <selectedIon> > > <selectedIonList count="1"> > <selectedIon> > <cvParam cvRef="MS" accession="MS:1000040" name="m/z" > value="445.34"/> > <cvParam cvRef="MS" accession="MS:1000042" name="intensity" > value="120053"/> > <cvParam cvRef="MS" accession="MS:1000041" name="charge state" > value="2"/> > ... > </selectedIonList> > > > I have delivered by problem in psi-ms-dev and spctools group but > couldn't come > up with concrete solution. Can someone clear me the term? > > -- > You received this message because you are subscribed to the Google > Groups "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to spctools- > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
