

Fixing the most common types of defects produced by students in Requirements workshops.
ELUCIDATE SOFTWARE PRO
TIGER PRO performs the following functions:
ELUCIDATE SOFTWARE MANUAL
Note that additional manual correction greatly enhances quantitation accuracy.

ELUCIDATE SOFTWARE SOFTWARE
The open-access software Skyline is used for automated quantitation. The software XiSearch, developed by our group, is used to identify cross-linked residue pairs, although the workflow is not limited to this search software. In this protocol, we demonstrate both label-free and isotope-labeled cross-linker-based workflows using the cross-linker bis(sulfosuccinimidyl)suberate (BS3).

A label-free workflow allows for application of a wide range of cross-linking chemistries and enables parallel comparison of multiple conformations. Distinguishing between minor and major changes requires a robust analysis based on carefully selected replicates and, when using isotope-labeled cross-linkers, replicated analysis with a permutated isotope-labeling scheme.

Small local conformational changes affect relative abundances of nearby cross-links, whereas larger conformational changes cause new cross-links to be formed. Cross-links provide information about structural changes that may be inaccessible by alternative technologies. It illuminates different structural states of proteins or protein complexes by comparing which residue pairs can be cross-linked in these states. This method has revealed induced conformational changes, composition shifts in conformational ensembles and changes in protein interactions. Quantitative cross-linking/mass spectrometry (QCLMS/QXL-MS) probes structural changes of proteins in solution. Crosslinking (quantitative), Publication.
