αA-WT and αA-G98R crystallin cross-links identified based on increase in mass corresponding to peptides cross-linked with deuterated and non-deuterated reagents.

The monoisotopic masses of the GPMAW identified peptide pairs (experimentala, theoreticalb and the calculated mass difference between the two in ppmf) are given. Subunit-subunit interaction sequencesc, d in αA-WT and αA-G98R are given. The crosslink type is indicated as X-link (between the subunits) and Int-X-link (within the subunits)e.
*Sequence confirmed by MS/MS analysis.
Ion pairs having similar retention time (RT) in LC and differing by mass of 4.03 Da were generated from the MS data using Excel spreadsheet. The theoretical m/z values for the cross-linked dipeptides were obtained from the software GPMAW (General Protein/Mass Analysis for Windows, Version 9.21, Lighthouse data; (http://www.gpmaw.com), using the MS X-link function for the respective protein and cross-linker and allowing two missed cleavage sites for trypsin. The experimental m/z values were searched against the theoretical m/z values using the Mass search feature of GPMAW set at 10 ppm.