The searches are from the same search engine. They're different msms runs. Thanks for the pipeline description.
On Wednesday, June 4, 2014 1:46:33 PM UTC-4, David Shteynberg wrote: > > Are the different Searches you draw different search engines or > different msms runs searched with you search engine? > > The general workflow is to combine the runs belonging to each > experiment and searched with one search engine (e.g. X!Tandem) > together with PeptideProphet. > Do this for each search engine you are running and combine the > PeptideProphet files with iProphet. Here is the approach in a > diagram: > > > Runs 1, 2, ..., n ----> Search 1 -----> PeptideProphet \ > | > ------> iProphet -----> PTMProphet > ----->ProteinProphet > -----> Search 2 -----> PeptideProphet / > ... > -----> Search m -----> PeptideProphet / > > Cheers, > -David > > On Wed, Jun 4, 2014 at 6:46 AM, Chris <[email protected] <javascript:>> > wrote: > > Hi everyone, > > > > I'm currently working on about 20 different mass spec runs and am new to > > using the TPP. I saw there are two approaches to using InterProphet. One > is: > > > > Search 1->...->InterProphet->downstream analysis > > Search 2->...->InterProphet->downstream analysis > > Search 3->...->InterProphet->downstream analysis > > Search 4->...->InterProphet->downstream analysis > > > > The other is: > > > > Search 1---------- > > \ > > Search 2----------- InterProphet->downstream analysis > > / > > Search N----------- > > > > Hopefully that little ansi diagram renders in however you are viewing > this. > > If not, it's basically showing the different of combining all your > analyses > > in a single interprophet run versus interprophet after every analysis. > Is > > there any difference to the 2 approaches? > > > > Chris > > > > -- > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > Visit this group at http://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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
