PABST peptide examples
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| PABST is a tool to help users select the best potential peptides to use for Mass Spectrometric identification of a set of proteins. It merges various data sources and evaluates the results based on user-tunable parameters. The current default parameter weightings are shown below, and the lower sections show links to example peptides along with comments to aid in the development of the selection algorithm. | PABST is a tool to help users select the best potential peptides to use for Mass Spectrometric identification of a set of proteins. It merges various data sources and evaluates the results based on user-tunable parameters. The current default parameter weightings are shown below, and the lower sections show links to example peptides along with comments to aid in the development of the selection algorithm. | ||
| - | + | <PRE> | |
| obs_bonus 1.0 # boost given to empirical_suitablity_score relative to theoretical_suitability_score | obs_bonus 1.0 # boost given to empirical_suitablity_score relative to theoretical_suitability_score | ||
| Line 18: | Line 18: | ||
| nQ 0.1 # Avoid N-terminal Q | nQ 0.1 # Avoid N-terminal Q | ||
| nxxG 0.3 # Avoid nxxG | nxxG 0.3 # Avoid nxxG | ||
| - | + | </PRE> | |
Revision as of 19:19, 22 April 2009
PABST is a tool to help users select the best potential peptides to use for Mass Spectrometric identification of a set of proteins. It merges various data sources and evaluates the results based on user-tunable parameters. The current default parameter weightings are shown below, and the lower sections show links to example peptides along with comments to aid in the development of the selection algorithm.
obs_bonus 1.0 # boost given to empirical_suitablity_score relative to theoretical_suitability_score C 0.3 # Avoid C D 1 # Slightly penalize D or S in general? DG 0.5 # Avoid dipeptide DG DP 0.5 # Avoid dipeptide DP M 0.3 # Avoid M NG 0.5 # Avoid dipeptide NG P 0.3 # Avoid P QG 0.5 # Avoid dipeptide QG S 1 # Slightly penalize D or S in general? W 0.1 # Avoid W Xc 0.5 # Avoid any C-terminal peptide nE 0.4 # Avoid N-terminal E nGPG 0.1 # Avoid nxyG where x or y is P or G nQ 0.1 # Avoid N-terminal Q nxxG 0.3 # Avoid nxxG
https://db.systemsbiology.net/devDC/sbeams/cgi/shortURL?key=c87rxtje
Protein: ALCAM, moderate number of observations
https://db.systemsbiology.net/devDC/sbeams/cgi/shortURL?key=xsp03v1h
Protein with tons of observed peptides, lots of them NT or MC.
https://db.systemsbiology.net/devDC/sbeams/cgi/shortURL?key=h5bwnrt2
Protein with many fewer observations
https://db.systemsbiology.net/devDC/sbeams/cgi/shortURL?key=s2kvwg9r
Protein with moderate number of obs, mixed MGL/SGL
