Hello, I would like to report a problem with msconvert. Brief description ============
msconvert does not extract HCD energy from Thermo RAW files. Background ========== HCD energy is *almost* always present in RAW file HCD ms/ms spectra. NCD "energy" is *always* present in HCD ms/ms spectra. That is, two energies (NCD and HCD) may be present in a HCD ms/ms spectrum. These two energy values are usually different. The units of HCD activation energy, according to RAW file contents, are eV. The units of NCD energy are percent (%). To derive HCD from NCD, one seems to need the charge used by the instrument software and m/z of the isolation range center. The actual formulas are unknown to me. It is also unknown to me if these formulas are the same for, for example, Orbitrap Velos and Q-Exactive. I have no information about contents of RAW files with mass spectra measured on Thermo Exactive (without Q), which may use HCD. Problems ======== 1. HCD energy is not read by msconvert from Thermo RAW files. 2. HCD energy is not output into mzXML or mzML files by msconvert. 3. The fact that the activation method name in mzML file is <cvParam cvRef="MS" accession="MS:1000422" name="*high-energy collision-induced dissociation*" value=""/> is accompanied by NCD value (not HCD value) in erroneous units, electronvolt, <cvParam cvRef="MS" accession="MS:1000045" name="*collision energy*" value=" *28.0*" unitCvRef="UO" unitAccession="UO:0000266" unitName="*electronvolt* "/> is unfortunate. How to read HCD energy from a RAW file =============================== >From my limited experience, there are two methods, usually only one works. 1. In Q-Exactive, Trailer Extra string named "HCD Energy eV:" may contain a string like this "24.243" 2. In Orbitrap Velos, Trailer Extra string named "FT Analyzer Message:" may look like this "MCal=29d RF=600V *HCD=35eV* Lock(inj371.1, NOT FOUND, t=1s, +0.067ppm)" Here HCD value seems to be always an integer. Sometimes the value is zero due to the rounding. Sometimes it is missing. Therefore, zero cannot be used to mark the value as missing. Unfortunately, I do not have information about RAW files produced by other Thermo instruments that employ HCD activation method. Thank you. Dmitrii -- 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.
