Hi,
The workflow I am trying to implement is, given a list of MS/MS peaks, can I
segment out the MS1 signal representing the peptide identified by that MS/MS
peak? (A single charge state representation is sought, meaning if the same
peptide is multiply charged, generating multiple MS/MS peaks, I just want to
map each MS/MS peak back to the single 3-d MS1 isotopic pattern corresponding
to it).
Right now I am doing the following:
1) Raw Data Methods->Raw Data Import. Open the mzML file.
2) Raw data methods-> Peak Detection->MS/MS Peak Builder.
3) Click on the first item under "Peak lists" in the right column. Peak List
Methods-> Peak Extender.
As you already realized, this workflow only gives you a single isotope (the
precursor ion) from each MS/MS spectrum. There is no method in MZmine to extend
this to the whole isotope pattern.
You can start with a different peak detection method (e.g. the Chromatogram
builder), which will detect all peaks at the MS1 level, and those you can group
together into isotope patterns by the Isotope Grouper module.
Tomas
===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
WWW: https://groups.oist.jp/g0
TEL: +81-98-966-8684
Fax: +81-98-966-2890
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