System and method for high throughput mass spectrometric analysis of proteome samples

A subsystem for preparing a specimen containing the proteome for analysis by mass spectrometry, comprising:

• a protein separation module;
• and
• a matrix processing module,
• wherein the protein separation module and the matrix processing module are in fluid communication with one another.

A method of analyzing a specimen containing the proteome by mass spectrometry, comprising:

• injecting a protein extract obtained from the specimen into a protein separation module to separate the protein extract into protein fractions having discrete molecular masses, wherein the separation is effected using a continuous SDS-PAGE gel column and the protein fractions having discrete molecular masses are eluted in solution form the continuous SDS-PAGE gel column and collected into a collection chamber having a negatively charged acrylamide trap;
• flowing the collected protein fractions having discrete molecular masses into a matrix processing module in fluid communication with the protein separation module to produce a matrix-free, protein-containing eluate, wherein the matrix processing module comprises an AF4 device having a miniaturized channel with one of the following properties:
• a length in the range from about 3.0 cm to about 10.0 cm, a width in the range from about 0.20 cm to about 1.00 cm and a height (thickness) in the range from about 10 microns to about 300 microns;
• or
• a volume in the range from about 3×10−6 cm3 to about 1.5×10−3 cm3 and a surface area in the range from about 0.30 cm2 to about 5.00 cm2;
• wherein the matrix processing module is configured to remove matrix components that interfere with mass spectrometry analysis of proteins;
• and
• flowing the matrix-free protein-containing eluate into a mass spectrometer in fluid communication with the matrix processing module to analyze protein.