Hi Elkan, every converter will do things a little differently. It’s hard to say which is better. I think we did some tests a while back and the SCIEX conversion of 5600 DDA data yielded slightly more IDs than with msconvert converter, but they were pretty similar. For most datasets, it should not matter much. I think SCIEX’s converter can produce mzML files as well, so I would recommend mzML instead of MGF. You could do both and compare. But you’ll likely be fine just to pick one and go with it.
In reviewing some notes I have, it looks like the msconvert tool does not have access to the precursor charge states, while the SCIEX converter does. So the SCIEX convert to mzML is probably the best option because you will get charge states, while a search with msconverted mzML will be guessing charge states. Just a problem with the SCIEX API that msconvert has access to. Regards, Eric *From:* spctools-discuss@googlegroups.com [mailto: spctools-discuss@googlegroups.com] *On Behalf Of *Elkan Dong *Sent:* Tuesday, October 24, 2017 10:08 PM *To:* spctools-discuss <spctools-discuss@googlegroups.com> *Subject:* [spctools-discuss] Peptide identification using AB SCIEX Raw data 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout. -- 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
