High Confidence Identification of Cross-Linked Peptides by an Enrichment-Based Dual Cleavable Cross-Linking Technology and Data Analysis tool Cleave-XL.

Cleavable cross-linking technology requires further MS/MS of the cleavable fragments for unambiguous identification of cross-linked peptides. These spectra are sometimes very ambiguous due to the sensitivity and complex fragmentation pattern of the peptides with the cross-linked residues. We recently reported a dual cleavable cross-linking technology (DUCCT), which can enhance the confidence in the identification of cross-linked peptides. The heart of this strategy is a novel dual mass spectrometry cleavable cross linker that can be cleaved preferentially by two differential tandem mass spectrometry methods, collision induced dissociation and electron transfer dissociation (CID and ETD). Different signature ions from two different mass spectra for the same cross-linked peptide helped identify the cross-linked peptides with high confidence. In this study, we developed an enrichment-based photocleavable DUCCT (PC-DUCCT-biotin), where cross-linked products were enriched from biological samples using affinity purification, and subsequently, two sequential tandem (CID and ETD) mass spectrometry processes were utilized. Furthermore, we developed a prototype software called Cleave-XL to analyze cross-linked products generated by DUCCT. Photocleavable DUCCT was demonstrated in standard peptides and proteins. Efficiency of the software tools to search and compare CID and ETD data of photocleavable DUCCT biotin in standard peptides and proteins as well as regular DUCCT in protein complexes from immune cells were tested. The software is efficient in pinpointing cross-linked sites using CID and ETD cross-linking data. We believe this new DUCCT and associated software tool Cleave-XL will advance high confidence identification of protein cross-linking sites and automated identification of low-resolution protein structures.

Mass spectrometry cleavable strategy for identification and differentiation of prenylated peptides.

Prenylation of protein (farnesylation and geranylgeranylation) is involved in several human cancers, such as pancreatic, colon, and acute myeloid leukemia as well as Hutchinson-Gilford progeria syndrome (HGPS), a genetic disease that is associated with premature aging for children. Current biochemical methods are not very efficient in identifying and differentiating large-scale prenylations in vivo or in vitro. There are limited methods available for large-scale detection of prenylated proteins using mass spectrometry and no methods currently available which can distinguish farnesylation and geranylgeranylation modification in a single experimental setup. In this study, a simple and novel method for detection and distinction of large-scale prenylated peptides using mass spectrometry-cleavable approaches was developed. The method utilizes simple chemistry on the prenyl group and cleavable properties of a sulfoxide group in the gas phase to produce a signature mass spectrum during tandem mass spectrometric events. The characteristic masses lost from the modified prenylated peptides distinguished the types of prenylation. We also introduced epoxy groups in the prenylation sites of the proteins to make them more hydrophilic and enrichable from complex samples. Stability of the epoxide group was also studied under liquid chromatography-mass spectrometry (LC-MS) conditions. The proof-of-concept of this method was established using prenylated peptides which mimicked the prenyl motifs in the proteins. We believe this method will advance the identification and differentiation of the types of prenylation in proteins in large-scale studies and will improve significantly our knowledge of the mechanism of cancer, cancer treatments, and diagnosis.