Dear all, I have raw data derived from AB SCIEX TripleTOF 5600 and protein identification results obtained from ProteinPilot using MGF files converted by AB SCIEX MS Converter. Now I want to use other search engines like Comet or X!Tandem to search the data again. So I converted to raw data to ..mzML files using ProteoWizard MSConvert and then searched by Comet. The question is that I found the spectra in ..mzML files are different with those in MGF peak lists generated by AB SCIEX MS Converter, what should I do? Still use ..mzML files generated by MSConvert or use AB SCIEX's MGF peak list? The helper of AB SCIEX MS Converter says that a signal processing procedure is applied when the converter is used to convert raw data to MGF peak list. Can I consider this as a preprocessing procedure of AB SCIEX search engine (i.e., ProteinPilot) to improve the identification? If so, I think I should use the ..mzML as Comet applies its own preprocessing procedure. But if not, I will use AB SCIEX's MGF peak list and skip the preprocessing procedure when Comet is used. How can I do this?
Can you help me on this? Thanks. Elkan -- 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
