Biopolymers & Proteomics Laboratory

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

Bldg 76 Room 181

Telephone: 617-253-7038



We use a Bruker model MicroFlex MALDI-TOF (matrix-absorption laser desorption instrument time-of-flight) to mass analyze peptides, protein, small molecules, polymers, DNA/RNA, conjugates, drugs and other biomolecules. The practical range mass range is between approximately 70 and 170,000 Da. The amount of sample needed for analysis ranges from high attomole upward. We typically load 1 pmole.

Analytes can also be fragmented on this MALDI by a process called post-source decay.

Sample Requirements

Samples can be dry or in solution by must be free of detergent with few exceptions e.g. Octyl-B-D-glucopyranoside. As a rule, we load the sample in a total volume of 1 ul that should be no greater than 1 mM salt. For example, if your sample is in 150 mM NaCl at a concentration of 150 pmol per ul we can dilute it 1:150 and load 1 ul. We can also desalt your sample using ZipTips, SCX resin (DNA/RNA) or reverse phase HPLC.

There are hundreds of MALDI matrices and we track which matrices work with which samples but if your sample is unique please attempt to provide a possible reference or at least the molecular structure to help us select the proper matrix.


In MALDI mass spectrometry the analyte is mixed with a protonating or deprotonating matrix solution and dried to crystal formation. A 337 nm nitrogen laser is fired at the sample-matrix crystals simultaneously with a high voltage pulse.  With proteins, a proton then jumps from the matrix to the analyte causing it to be positively charged in a vacuum environment containing a 20,000 volt differential electrical field. The time it takes for sample ion to drift through the vacuum flight tube to a detector is proportional to the molecular weight. See the Sigma-Aldrich list of matrices and applications by searching the Sigma web page for “Matrix Substances for MALDI-MS”.

MALDI is not quantitative in our hands. We recommend that you use ESI mass spectrometry or HPLC if quantitative data is required.

Data Output

MALDI data is given in mass-to-charge ratio (m/z) units where the charge state is (almost) always +1 or -1 proton. A molecule with a MW of 1000.0 would be displayed as 1001.0 (M+H)+  if analyzed in positive mode and that same molecule would be displayed as 999.0 (M-H)- if analyzed in the negative (deprotonated) mode.

Data is pasted into a text document and emailed. Original instrument printouts can be delivered or scanned and emailed. We can email the raw data file and freeware MALDI analysis software (M over Z) can be used to analyze the spectra to your personal specifications on your PC.

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