Generate a PRM transition file for analysis of cross-links with Skyline.

For tutorial more information pertaining to Parallel Reaction Monitoring (PRM) and XL-MS, refer to these papers/resources:

2017/03/24 update: To open the created transition file in Skyline: go to File > Import > Transition List, and select the csv file.

Single PRM Transition Input:

Cross-linker Type:

Precursor Charge State:

Peptide A:

Peptide B:

Batch PRM Transition input:

Select batch file input:

Batch input files should be space or tab-separated ('.txt') files of the format:
short_arm_mass   long_arm_mass
peptideA   peptideB   pepmodA   pepmodB   charge_state
peptideA   peptideB   pepmodA   pepmodB   charge_state
peptideA   peptideB   pepmodA   pepmodB   charge_state

Modification masses should include be the stump mass for cross-linkers (e.g. BDP-NHP: 197.0324 or DSSO: 54.0111).
For non-cleavable cross-linker, the modification mass should include the mass of the cross-linker plus the mass of the other peptide.
Format of modification is: mass@position, i.e. "197.0324@2,57.0215@3".
The charge state is the precursor charge of the intact cross-linked molecule.

For non-cleavable cross-linkers, set the short_arm_mass and long_arm_mass to zero e.g. "0.0 0.0" and make the encoded modification at the cross-link site the mass of the other peptide plus mass of cross-linker. See the DSS input file below for an example.

Example of input (BDP-NHP crosslinker):
197.032422 948.437502
QKAEADKNDK QKAEADKNDK 197.0324@2 197.0324@2 4
MEESKCK KVEKVTISNR 197.0324@5,57.0215@6 197.0324@4 5

Download a brief example DSS input file.

Download a brief example DSSO input file.

Download a brief example BDP-NHP input file.

Download corresponding example BDP-NHP transition output file here.

**Developed by Jimmy K Eng (UWPR) and Devin K Schweppe (Bruce Lab)**