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 <sma.banijam...@gmail.com> 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 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.
