PABST peptide examples

From SPCTools

 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