There are some issues in using MSPathfinderT to search thermo .raw EThcD data.
I understand that Informed Proteomics would handle EThcD spectra as ETD spectra, for ETD is the major driving fragmentation force in EThcD.
Yet, I found out that when thermo .raw file is used to generate the .pbf data, MSPathfinderT would automatically assign HCD to EThcD spectra and it would only handle the b y ions. For these ions were not the majority, most of the PrSM had bad scores.
I have tried to input -act ETD (i.e. specify the activation method is ETD) in the command line, but the same problem will still be resulted. (Search result and raw file here)
I pondered that this problem may due to the .raw format. Therefore, I tried to first convert the .raw file to .mzml then use it to generate a .pbf to do the search again. This time it had worked. MSPathfinderT were able to handle the MS2 spectra as ETD spectra (i.e. search c z ions), with or without my specification of -act ETD. (Search result and mzml file here)
Another Issue is that the IcTda or IcTarget #matched fragment ions does not seem to match with that reported in LCMSSpectator. For example in this PrSM, it was reported that the #Matching ions is 74.
Nonetheless, as reported in the LCMSSpectator, there should only be 68 ions. In some cases, there were more ions reported in LCMSSpectator than in the IcTda or IcTarget
Lastly, since MSPathfinderT can now support UVPD, which has even more ion types than EThcD, would MSPathFinderT able to support EThcD (i.e. to search for all b y c z ions) in the near future? I know it is quite a bit to ask but in the case of highly modified proteins like histones, thorough fragment information is quite important to locate the PTMs and sequence variants. So adding this function would definitely help this field a lot.
There are some issues in using MSPathfinderT to search thermo .raw EThcD data.
I understand that Informed Proteomics would handle EThcD spectra as ETD spectra, for ETD is the major driving fragmentation force in EThcD.
Yet, I found out that when thermo .raw file is used to generate the .pbf data, MSPathfinderT would automatically assign HCD to EThcD spectra and it would only handle the b y ions. For these ions were not the majority, most of the PrSM had bad scores. I have tried to input -act ETD (i.e. specify the activation method is ETD) in the command line, but the same problem will still be resulted. (Search result and raw file here)
I pondered that this problem may due to the .raw format. Therefore, I tried to first convert the .raw file to .mzml then use it to generate a .pbf to do the search again. This time it had worked. MSPathfinderT were able to handle the MS2 spectra as ETD spectra (i.e. search c z ions), with or without my specification of -act ETD. (Search result and mzml file here)
Another Issue is that the IcTda or IcTarget #matched fragment ions does not seem to match with that reported in LCMSSpectator. For example in this PrSM, it was reported that the #Matching ions is 74.
Nonetheless, as reported in the LCMSSpectator, there should only be 68 ions. In some cases, there were more ions reported in LCMSSpectator than in the IcTda or IcTarget
Lastly, since MSPathfinderT can now support UVPD, which has even more ion types than EThcD, would MSPathFinderT able to support EThcD (i.e. to search for all b y c z ions) in the near future? I know it is quite a bit to ask but in the case of highly modified proteins like histones, thorough fragment information is quite important to locate the PTMs and sequence variants. So adding this function would definitely help this field a lot.