A method for identifying the presence or absence of a protein or polypeptide analyte compound within a liquid sample comprising a mixture of compounds that includes a plurality of protein compounds or a plurality of polypeptide compounds or pluralities of both protein and polypeptide compounds, the method comprising: (a) introducing a portion of the liquid sample into an electrospray ionization source of a mass spectrometer; (b) forming positively charged ions of the mixture of compounds of the portion of the liquid sample by electrospray ionization, the positively charged ions comprising a plurality of ion species; (c) isolating a first subset of the ion species comprising a first mass-to-charge ( m / z) ratio range that includes an m / z ratio of a particular predetermined multiply-protonated molecular species of the analyte compound; (d) generating a plurality of first-generation product ion species from the isolated first subset of ion species by causing the isolated first subset of ion species to be reacted, for a predetermined time duration, with reagent anions that, upon reaction, extract protons from each of one or more ion species that comprises a protonated molecular species of a protein or polypeptide compound; (e) generating a mass spectrum, using a mass analyzer, of either the first-generation product ion species or of second-generation product ion species generated from the first-generation product ion species; (f) recognizing, from the mass spectrum of either the first-generation or the second-generation product ion species, a set of one or more m / z ratios that are diagnostic of the protein or polypeptide analyte compound; and (g) identifying the presence of the analyte compound within the sample if the set of one or more m / z ratios is identified in the mass spectrum, wherein the step (f) of recognizing the set of one or more m / z ratios that are diagnostic of the protein or polypeptide analyte compound employs a mathematical analysis algorithm in which intensities of peaks observed in the mass spectrum are represented as Boolean values and the m / z value of each peak is represented by a variable, T ( m / z), where T ( m / z) = ln(( m / z) -M proton) and M proton is the mass of a proton. (a) introducing a portion of the liquid sample into an electrospray ionization source of a mass spectrometer; (b) forming positively charged ions of the mixture of compounds of the portion of the liquid sample by electrospray ionization, the positively charged ions comprising a plurality of ion species; (c) isolating a first subset of the ion species comprising a first mass-to-charge ( m / z) ratio range that includes an m / z ratio of a particular predetermined multiply-protonated molecular species of the analyte compound; (d) generating a plurality of first-generation product ion species from the isolated first subset of ion species by causing the isolated first subset of ion species to be reacted, for a predetermined time duration, with reagent anions that, upon reaction, extract protons from each of one or more ion species that comprises a protonated molecular species of a protein or polypeptide compound; (e) generating a mass spectrum, using a mass analyzer, of either the first-generation product ion species or of second-generation product ion species generated from the first-generation product ion species; (f) recognizing, from the mass spectrum of either the first-generation or the second-generation product ion species, a set of one or more m / z ratios that are diagnostic of the protein or polypeptide analyte compound; and (g) identifying the presence of the analyte compound within the sample if the set of one or more m / z ratios is identified in the mass spectrum, wherein the step (f) of recognizing the set of one or more m / z ratios that are diagnostic of the protein or polypeptide analyte compound employs a mathematical analysis algorithm in which intensities of peaks observed in the mass spectrum are represented as Boolean values and the m / z value of each peak is represented by a variable, T ( m / z), where T ( m / z) = ln(( m / z) -M proton) and M proton is the mass of a proton.