Protein-works: Protein Mapping

MS Bioworks protein mapping service (MSB-03) enables the interrogation of the entire sequence of a protein. This service is ideal for finding novel PTMs, identifying regions of interest inaccessible to trypsin alone or confirming a primary sequence. The basic experimental workflow for our protein mapping service is presented below.

Separate instances of an incurred sample are digested using a panel of three proteases and analyzed by nanoscale LC/MS/MS on a LTQ Orbitrap Velos mass spectrometer. Data are searched and protein identified using Mascot (Matrix Science) and processed via the Scaffold software (Proteome Software). We provide a report summarizing the proteins identified in a sample and a summary file to allow independent data interrogation.

Our protein mapping service is compatible with your sample preparation buffers and we recommend submitting a minimum of 100ng of material.

Protein mapping of circadian locomotor cycles protein kaput (CLOCK) in Drosophila
The protein in this example was submitted as part of a complex sample, the sample was fractionated using SDS-PAGE and the region of interest excised. This was repeated three times and the excised bands were digested with trypsin, chymotrypsin and pepsin. The combined data are presented below.

MSB-3 can be ordered directly from our online ordering system, here.