Though MALDI successfully monitored the modifications with KYL on one phage displayed peptide, we reported previously that the reactivity in phage libraries could change from clone to clone by factor of 400, hence, it is crucial to measure the modification on the phage libraries in addition to the assessment of the reaction on individual clones. We measured chemical modification of libraries using previously reported biotinylation procedure followed by streptavidin capture to distinguish modified from unmodified phages. We tested different reaction conditions using the library SX3CX5C (X = 19 AA without Cysteine, 10 10 random peptides), into this library we mixed wild-type (WT) phage as negative control (Figure ). Library clones transduced LacZa reporter and form blue plaques in the presence of IPTG/Xgal, whereas WT phage lacking the reporter produces white plaques in these conditions. This blue/white assay monitored non-specific modification on phage coat proteins. Phage library and WT mixture were reduced by TCEP, then reacted with 0.01 mM, 0.1 mM, 0.2 mM and 1 mM of KYL for 30 min in TB buffer, pH 8.6. To quantify the modification by KYL, phages were then treated with an aldehyde reactive aminooxybiotin (AOB) (Figure ), allowing the aldehyde containing phages to be pulled down by streptavidin magnetic beads (Figure ). We observed that high concentration of linchpin (1 mM) resulted in phage death and non-specific modification (Figure , S27h) and similar detrimental effects have been previous reported by Heinis and co-workers. Overall, 0.1 mM of KYL was found to be optimal to balance between low toxicity to phage, low non-specific modification, and high modification rate (Figure ). Furthermore, to measure the conversion of aldehyde-peptide to Malins bicycle, AOB was applied again after bicyclization step to detect the remaining unreacted aldehyde-phages. No biotin capture was observed, indicating all 78 % aldehyde-phages were consumed (Figure ).