Hi David Thanks for the prompt reply! RTCatalog sounds like an interesting tool! I just took a quick look at the command (RTCatalogParser) in linux and apparently it also accepts sptxt as input. Does it mean that I can use the empirical retention times of each peptide in a spectral library/processed-pepXML for comparison with the new hits that I run PepPro on them?
Many Thanks, Ali On Thursday, January 5, 2017 at 2:42:14 PM UTC-5, David Shteynberg wrote: > > Hello Ali, > > The RT model in PeptideProphet can be used to boost the probabilities of > peptides close to their expected RT and reduce the probabilities of > peptides far from their expected RT. RTCalc implements two algorithms for > RT prediction. One is based on an Artificial Neural Network (ANN) using > sequence information with other factors, the other uses Linear Regression > (LR) modeling, the default mode of RTCalc is LR. You can train RTCalc > using your own set of peptides, but there is an existing model that it is > shipped with. RTCatalog is a different tool for building catalogs of > measured peptide Retention Times based on TPP processed data, it has many > options such as run by run RT correction based on landmark peptides. RTCalc > can be accessed in Petunia "RT Training" "RT Prediction" pages, while > RTCatalog is an advanced tool which must be used on the commandline at this > time. > > -David > > - > > On Thu, Jan 5, 2017 at 10:42 AM, Ali <[email protected] <javascript:>> > wrote: > >> Dear all >> >> I can't find a good place to completely understand RT-RTCAT options in >> peptide prophet. This is all that I've understood. Correct me if I am wrong: >> >> RT model compares peptide's retention times with those learned using an >> ANN or a LR model. The learned retention times can be produced using RT >> Training tool in TPP GUI. The model will eventually reward or penalize hits >> by comparing their retention time with those from the model. Here are my >> questions: >> >> >> 1. Is this the algorithm of the ANN:* Improved Peptide Elution Time >> Prediction for Reversed-Phase Liquid Chromatography-MS by Incorporating >> Peptide Sequence Information : Konstantinos Petritis et al.* >> 2. Is there a paper where I can read exactly how RT model works? >> 3. Can I provide my own set of retention times for RT model instead >> of using RTCalc? >> 4. What is RTCAT? What is the catalog file? How does it look like? >> How can I create it? >> >> Thank you very much. >> >> Sincerely, >> Ali >> >> >> -- >> 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 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.
