A method for measuring the relative amounts of a first and a second compartment of a biological sample comprising: i) selecting a first monitor peptide that is proteotypic for a first protein whose amount in said sample is contributed predominantly by said first compartment, ii) selecting a second monitor peptide that is proteotypic for a second protein whose amount in said sample is contributed predominantly by said second compartment, iii) digesting said sample by means of a proteolytic process to produce a digest, iv) adding to said digest labeled versions of said first and second peptides, differing respectively from said first and second peptides by a mass increment, in known amounts, v) measuring the amounts of said first monitor peptide and said labeled version of said first monitor peptide using a mass spectrometer, dividing said measured amount of said first monitor peptide by said measured amount of said labeled version of said first monitor peptide to produce a first ratio, and multiplying said first ratio by the known amount of said labeled version of said first peptide to yield an amount of said first peptide in the digest, vi) measuring the amounts of said second monitor peptide and said labeled version of said second monitor peptide using a mass spectrometer, dividing said measured amount of said second monitor peptide by said measured amount of said labeled version of said second monitor peptide to produce a second ratio, and multiplying said second ratio by the known amount of said labeled version of said second peptide to yield an amount of said second peptide in the digest, vii) calculating the relative amounts of said first and second compartments in said sample using the relative amounts of said first and second peptides in the digest, together with previous measurements of the concentrations of said first peptide, or said first protein, in said first compartment and of said second peptide, or said second protein, in said second compartment. i) selecting a first monitor peptide that is proteotypic for a first protein whose amount in said sample is contributed predominantly by said first compartment, ii) selecting a second monitor peptide that is proteotypic for a second protein whose amount in said sample is contributed predominantly by said second compartment, iii) digesting said sample by means of a proteolytic process to produce a digest, iv) adding to said digest labeled versions of said first and second peptides, differing respectively from said first and second peptides by a mass increment, in known amounts, v) measuring the amounts of said first monitor peptide and said labeled version of said first monitor peptide using a mass spectrometer, dividing said measured amount of said first monitor peptide by said measured amount of said labeled version of said first monitor peptide to produce a first ratio, and multiplying said first ratio by the known amount of said labeled version of said first peptide to yield an amount of said first peptide in the digest, vi) measuring the amounts of said second monitor peptide and said labeled version of said second monitor peptide using a mass spectrometer, dividing said measured amount of said second monitor peptide by said measured amount of said labeled version of said second monitor peptide to produce a second ratio, and multiplying said second ratio by the known amount of said labeled version of said second peptide to yield an amount of said second peptide in the digest, vii) calculating the relative amounts of said first and second compartments in said sample using the relative amounts of said first and second peptides in the digest, together with previous measurements of the concentrations of said first peptide, or said first protein, in said first compartment and of said second peptide, or said second protein, in said second compartment.