The IECS offers proteomic analyses with the Waters Synapt G2 HDMS. The Q-TOF MS is capable of ion mobility separation with accurate mass data. The main use is the identification and quantification of proteins. The system is coupled to the nanoAcquity UPLC system allowing high-throughput analyses of complex protein and proteome samples using electrospray ionization. The system can also be converted to a MALDI source for specific analytes or for MALDI imaging.

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For superior duty cycles data independent MS/MS analyses (MSEE) is commonly run, but we also provide solutions for targeted approaches. The lockspray system allows mass accuracy of up to 1 ppm RMS.

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The Waters system also incorporates ion mobility separation that can be used to differentiate between different protein conformations and isomeric species. Furthermore, it allows a further separation of complex samples resulting in increased protein identifications.

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Our standard procedure is to digest protein and proteome samples prior to analysis and generic protocols are provided here.

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Quantitative and comparative analyses can be done with a variety of strategies including labelled strategies using SILAC or iTRAQ. However, the typically high protein coverage offered by MSE analysis is well suited for label-free proteome quantifications. For certain applications a pre-fractionation of proteome samples using e.g. 1D, 2D gel electrophoresis can be beneficial.

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We are also able to analyze a variety of other metabolites using either nanoESI, MALDI, standard ESI or Atmospheric Solids Analysis Probes (ASAP) as well as develop customized analytical approaches.