Project Information
Title:
Molecular Mapping of FXIIIa Crosslinks
Abstract:
Here we present characterization of fibrin clots generated in vitro and ex vivo to obtain molecular detail regarding the specificity of FXIIIa cross-linking sites and substrates. Clots were generated and analyzed from ex vivo generated clots using healthy volunteer whole blood (WB) and matching plasma (plsm1); Ex vivo from banked plasma in the presence of EDTA and citrate (Plsm2); and a in vivo mediastinal wound thrombi (SurgThrombi).
Notes:
FXIIIa is a transglutaminase that cross-links Gln to Lys residues (Q-K). The change in mass for the peptide pair is -NH3 (-17.026) as a result miscleaved peptides can give rise to cross-linked spectral matches when the wrong precursor is selected. It should be possible to manually confirm if these identifications are linear false matches. As a result, these identifications are suspect until validated.
HA digestion is not N|G specific, nor is N|X digestion complete. Best results were obtained when the number of possible mis-cleavages was kept high (4 or greater).
The fibrinogen gamma entry for FIBG-alpha or FIBGA just contains the sequence for the region where it differs from the fibrinogen gamma' sequence (as a tryptic peptide).
Results were filtered at 1% FDR further filtering can be performed here. E.Coli proteins (with approx. equal size to human entries) were used in addition to the decoy sequences generated by the search software for FDR calculations. This allowed for an additional assessment of the FDR filter used for spectral matching.
