Biopolymers & Proteomics Laboratory

The David H.Koch Institute for Integrative Cancer Research at MIT

Bldg 76 Room 181

Telephone: 617-253-7038

Mass Spectrometry and Proteomics


Which type of MS should I use?

Ion trap – We use this instrument almost exclusively for the identification of proteins from enzymatic digests at high sensitivity from e.g. 1D and 2D gel spots or unfractionated IP pull downs. It can also be used to analyze small molecules, protein up to approx. 35 kDa. and to fragment (MSMS) molecules below approx. 3000 Da. Samples are dissolved and infused via an HPLC system or sprayed in via nanospray needle or syringe.

MALDI-TOF - MALDI TOF is good for mass measurement of proteins up to 500 kDa., peptides, conjugates, nucleic acids up to 30 kDa, polymers and even small molecules. MALDI Mass Mapping, the enzymatic digestion of of two samples followed by differential analysis of their mass spec profiles, can be very informative. Accuracy is between 0.1 and 0.01%. This mass spectrometry depends on the creation of good crystals, and the data are proportional to the size and quality of the particular crystal hit with a laser. It is therefore not quantitative. The procedure is fast and can have accuracy of 5 ppm for peptides under 2500 daltons when using internal calibration. Larger molecules show less accuracy.

Q-TOF - Sample prep is similar to the Ion-trap. PPM accuracy using a model QSTAR instrument. Used primarily to analyze small molecules, protein up to approx. 80 kDa. and peptides. Mass spec sequencing/protein identification, post translational modification analysis and quantitative mass spec are typical uses. Please contact:

Please feel free to contact us if you have questions or to discuss specific items related to your projects