ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite

BMC Bioinformatics

Table 2 Mass additions for crosslinks cleavage products.

Reagent	Cleavable	Mclrest	Mclirest	Mcliploss	Mclohloss	Mcliloss
DTSP	DTT	87.99829	175.99657	-3.02349	103.99320	-2.01566
	CID	119.96981	-	-1.00727	72.02058	-
		54.01002	-	-1.00727	137.98037	-
EGS	NH₄OH	82.00548	164.01096	61.02895	162.05282	62.03678
BiPS	hν	278.07251	173.98091	-3.02349	103.99320	190.07422
		87.99829	173.98091	-3.02349	294.06743	190.07422
DNBDPS	DTT, 100°C	87.99829	175.99657	162.97852	269.99465	163.98581
TEABS	NH₄OH	82.00548	164.01096	488.21844	589.24121	489.22571

The masses of the cleaved crosslinks can be calculated using following formulas:
[M₁₂+H]⁺ = [M₁cl+H]⁺ + [M₂cl+H]⁺ +Mcliploss
[M₁OH+H]⁺ = [M₁cl+H]⁺ +Mclohloss
[M₁i+H]⁺ = [M₁icl+H]⁺ +Mcliloss
[M₁cl+H]⁺ = [M₁+H]⁺ +Mclrest
[M₁icl+H]⁺ = [M₁+H]⁺ +Mclirest
where H -- mass of proton; M₁, M₂ -- masses of free peptides; M₁₂ -- mass of inter-peptide crosslink; M₁OH -- mass of dead-end crosslink; M₁i -- mass of intra-peptide crosslink; M₁cl -- mass of cleaved dead-end or inter-peptide crosslink; M₁icl -- mass of cleaved intra-peptide crosslink; Mcliploss, Mclohloss, Mcliloss -- mass additions for cleaved inter-peptide, dead-end and intra-peptide crosslinks, respectively; Mclrest, Mclirest -- mass of cleaved portion of the crosslinking reagent for cleaved inter-peptide or dead-end and intra-peptide crosslinks, respectively.

ISSN: 1471-2105