Deconvolving isobaric reporter ion ratios

A method comprising:

• applying distinct isobaric tags to each of a plurality of samples;
• combining the samples;
• performing a chromatographic separation of species within the combined samples;
• isolating and fragmenting labeled parent ions within a m/z range to produce a plurality of reporter ions and structurally informative ions at a plurality of points along a chromatographic peak, each reporter ion corresponding to one of the isobaric tags, the structurally informative ions resulting from fragmentation of a peptide backbone of the labeled parent ion;
• determining intensities of the plurality of reporter ions and the structurally informative ions at the plurality of points along the chromatographic peak in the separation dimension;
• fitting the intensities of the structurally informative ions and the plurality of reporter ions at the plurality of points along the chromatographic peak to determine a contribution of interfering ions and a contribution quotient for the parent ion;
• and
• obtain a relative abundance of the parent species based on the contribution quotients for the parent ions for each of the plurality of samples.