Hi Eric, Thanks for your suggestion, it's very valuable for me.
I noticed that AB SCIEX assigned charge states to precursors, even fragments. But can I trust this? ProteinPilot tries several charge states for each tandem mass spectrum, so I think we can ignore those charges evaluated by AB. I am now setting very wide range of charge in Comet search. Thanks again. Regards, Ellen. 2017年10月25日 下午11:56，"Eric Deutsch" <[email protected]>写道： > 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:* [email protected] [mailto:spctools-discuss@ > googlegroups.com] *On Behalf Of *Elkan Dong > *Sent:* Tuesday, October 24, 2017 10:08 PM > *To:* spctools-discuss <[email protected]> > *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 [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. > > -- > 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. > -- 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.
