Table I Comparison of different protein extraction methods and the effect of including cell debris in the digestion step
Extraction-buffer detergentNumber of peptidesNumber of protein groups
Urea17,024 ± 1483,326 ± 20
SDC22,171 ± 4033,698 ± 18
ProteaseMAX29,884 ± 2284,465 ± 100
Including cell debris33,098 ± 2834,655 ± 51