Fig. 2.

Affinity enrichment improves detection of crosslinker-modified peptides. A, Diagram of the affinity-tag-based enrichment strategy. An SCX fraction containing a mixture of peptides and crosslinker-modified peptides is loaded onto a monomeric avidin column. Peptides that do not contain crosslinker are discarded in the flow-through and wash fractions whereas those that do are retained. These retained crosslinker-modified peptides are eluted from the column and collected (eluate) for subsequent LCMS analysis. A portion of the SCX fraction prior to enrichment (load) may also be saved for LCMS analysis to assess the improvement in crosslinker-modified species detected as shown in B. A comparison of Δ8.0502 Da doublet features found in MS1 for samples without (load) (B) and with (eluate) (C) enrichment shows ∼2.7 times as many doublet features with enrichment (D).