MS-Bridge

[…] xameric complex described above. The purified proteolytic fragments obtained after digestion, were characterized by spectroscopy and analyzed by Mass Spectrometry (MS) at the University of Edinburgh. MS-bridge prospector platform (http://prospector.ucsf.edu) was used for search and identification. The elemental composition of modified cysteines and/or the chromophore as crosslinking agent were use […]

[…] tesque) as internal standards and with α-cyano-4-hydroxycinnamic acid (Wako) as a matrix. Spectra were obtained using Ultraflex™ (Bruker Daltonics) in linear mode, and mass peaks were assigned using MS Bridge (University of California, San Francisco, CA). […]

[…] GO-203 with MUC1-CD, GO-203 was incubated with purified GST-MUC1-CD. The complexes were separated by SDS-PAGE and tryptic digests were analyzed by MALDI-TOF-MS (). Peptide identification was based on MS-bridge analysis of the tryptic digest MALDI-TOF data against the sequences of the 2 known components of the reaction, i.e. GST-MUC1-CD () and GO-203. The peptide dimer with a single disulfide bridg […]

[…] remnant moieties for d0- (i.e., A, S, T) or d10-DMSSO (i.e., A*, S*, T*) cross-linker, respectively. Initial acceptance criteria for peptide identification required a reported expectation value ≤0.1.MS-Bridge was used to confirm the identification of cross-linked peptides by mass mapping against bovine cytochrome C with the parent mass error set as ±10 ppm. The in-house program Link-Hunter is a r […]

[…] on Regional Proteomics Facility. Recovered peptides were subjected to matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, and the results analyzed using the UCSF MS-Bridge webpage. To delineate the boundary of the trypsin- and elastase-stable catalytic domain, liquid chromatography (LC) mass spectrometry was performed on a 3Q mass spectrometer (Micromass) equi […]

[…] ss-links. For example, not all possible ion types for each peptide are considered.Another strategy that, up to now, has only been used with restricted databases is implemented in the tools Batch-Tag, MS-Bridge, and MS-Product that are part of the Protein Prospector package () and Popitam (CXMS pipeline) (). Both are based on the rationale that cross-linked peptides may be considered as a single li […]