Protein Identification

Protein identification is performed using the sensitive technique of nano LC/MS/MS on either an LTQ or LTQ Orbitrap XL mass spectrometer. Protein samples may be submitted in a gel or solution and are first digested robotically using trypsin to create a peptide mixture (alternate enzymes may be employed if necessary). Peptides are then injected on our custom-designed LC column set-up and eluted into the mass spectrometer where MS and MS/MS are performed. Years of experience optimizing digestion, sample handling, chromatography and mass spectrometer conditions allow us to achieve unparalleled levels of sensitivity and coverage. Product ion data is searched in-house using forward and reversed database searching methods to allow assessment of false discovery rates and ensure only correct protein identifications are reported. Search results are parsed into the Scaffold™ visualization software to allow further validation of protein assignments through the ProteinProphet™ and PeptideProphet™¹ tools. We give both tabulated reports and Scaffold™ files (accessible through a free viewer) to clients allowing for full inspection of the data.

In the rare case that we cannot generate a list of tryptic peptides by LC/MS/MS we will only charge you for the in-gel digestion. If a list of tryptic peptides is generated and it does not match to anything in the protein databases we offer de novo sequencing services.

(1) Keller, A. et al., Anal. Chem., 74, 5383 (2002)

Downloads:

• Example protein identification report on 1D band
• Scaffold™ file accompanying example protein identification report (note: 13Mb in size)
• Free Scaffold™ file viewer from Proteome Software