SRM Collider
version 1.4
Hannes Röst 2012

The SRMCollider is a program that will take your input transitions and compare them to all other transitions in a given background proteome and find interferences. It will report these interferences on a per-peptide basis, allowing a researcher to identify peptides that share many transitions with the target peptide.


arbitrary units

Th

Th

Th

Th

amu

Check that interfering signal can actually hold charge (e.g. 2+ charge)

oxidized Methionines deamidated Asparagines

Background Ion Series

aions
aMinusNH3
bions
bMinusH2O
bMinusNH3
bPlusH2O
cions
xions
yions
yMinusH2O
yMinusNH3
zions
MMinusH2O
MMinusNH3

Please note that this server may take some time to respond to the first query, this is due to the time needed to populate the MySQL cache with the corresponding indices. After running a couple of peptides (10-20), the computation time per peptide should be well below 100 ms for yeast (other proteomes are bigger and might take longer, also non-default options like higher order UIS might increase the computing time).

* This will print out a list of all UIS combinations of transitions for all peptides. Preferably, only combinations of less than 5 transitions are considered, otherwise the result might get quite large.