Relative retention time predicting software

[DJ]

There used to be a fantastic web-based sequence-specific retention calculator for peptides (without any prior retention data inpu). This algorithm calculates based on AA sequence, and my experience has been five-start using it.

But as of a few days ago, it (and all its previous, still functional) websites have vanished. Since Drylab's license key costs more than my car is worth.. I wonder if the days of trotting over there for highly accurate order of retention./relative retention calculations are over?

Unlike Drylab, I'm afraid this colonial's recipe won't come as easy as finding a calculator with numerical solver. Data are from 5,000 tryptic peptides.

[Kostas Petritis]

There is a really nice software you can download for free from http://omics.pnl.gov/software/NETPredictionUtility.php.

The software provides normalized retention times for peptides and includes several algorithms including ours (Petritis and Kangas) as well as Krokhin and Mant.

I'm sure that one of those will work just fine for your application.

Taken from the website:

"Normalized Elution Time (NET) Prediction Utility

The NET Prediction Utility can be used to compute predicted normalized elution time (NET) values for a list of peptide sequences. The elution times are intended for use with reversed phase liquid chromatography (e.g. using C18 coated silica particles) analyses, and are used in our lab for alignment of LC-MS and LC-MS/MS datasets to one another (using the predicted elution times to form a master in-silico dataset to align each dataset to). The predicted elution times are also used by the Protein Digestion Simulator when calculating the number of uniquely identifiable peptides within an input file using both mass and NET. For more information on the utility of predicted elution times, see the References listed below.

The software has now been expanded to include the Kangas / Petritis retention time prediction algorithms for both LC retention time prediction and strong cation exchange (SCX) fraction prediction (using a 0 to 1 scale). For SCX fraction prediction, you have the option of using the SCX Prediction Utility, which is a variant of the NET Prediction Utility and only computes predicted SCX fraction values.

The NET Prediction Utility reads the peptides from a text file containing one peptide sequence on each line. The output file includes the peptide sequence plus the predicted NET value (and/or predicted SCX value) using one or all of the prediction algorithms:

Kangas/Petritis LC retention time model
Kangas/Petritis SCX fraction model
Krokhin hydrophobicity model
Mant hydrophobicity model"