Method and System for Detecting Peptide Peaks in HPLC-MS Signals

A method for noise rejection and detection within the data of a measurement signal (11) generated by the combination of a chromatograph (2) and a mass spectrometer (3), said data identifying the intensity values of the proteins contained in a biological sample, said measurement signal (11) having at least one peak value (24) combined with stochastic and/or chemical noise (12a, 12b), said peak value (24) being representative of a peptide peak that can be found in said measurement signal (11), said method comprising the steps of:

• providing a Single Ion Chromatogram (SIC) representative of the elution values at a specific mass value (m/z) of said measurement signal (11);
• performing a first wavelet decomposition (15) of said values of said Single Ion Chromatogram (SIC) to generate a first processed vector (16) representative of the smoothed intensity values of the Single Ion Chromatogram (SIC);
• performing a second wavelet decomposition (17) of said values of said Single Ion Chromatogram (SIC) to generate a second processed vector (18) representative of said Single Ion Chromatogram (SIC) cleaned of any oscillations generated by stochastic noise (12b);
• setting a threshold value (5);
• processing said first processed vector (16) and said second processed vector (18), the latter accounting for said threshold value (S), to generate a third processed vector (19) identifying the baseline value of said Single Ion Chromatogram (SIC) so as to reject the chemical noise. wherein it further comprises the step of processing said Single Ion Chromatogram (SIC) and said second (18) and third (19) vectors to generate a filtered vector (20) identifying a value (z,) of said peptide peak (24) below said stochastic and/or chemical noise (12a, 12b).

A computer tool for processing data representative of the intensity values of a measurement signal (11), said measurement signal (11) having at least one peak value (24) combined with a stochastic and/or chemical noise (12a, 12b), said computer tool being adapted to be directly loaded into memory of a computer device, comprising portions of program code susceptible of implementing the method when run on said computer device, said method being for noise rejection and detection within the data of a measurement signal (11) generated by the combination of a chromatograph (2) and a mass spectrometer (3), said data identifying the intensity values of the proteins contained in a biological sample, said measurement signal (11) having at least one peak value (24) combined with stochastic and/or chemical noise (12a, 12b), said peak value (24) being representative of a peptide peak that can be found in said measurement signal (11), said method comprising the steps of:

• providing a Single Ion Chromatogram (SIC) representative of the elution values at a specific mass value (m/z) of said measurement signal (11);
• performing a first wavelet decomposition (15) of said values of said Single Ion Chromatogram (SIC) to generate a first processed vector (16) representative of the smoothed intensity values of the Single Ion Chromatogram (SIC);
• performing a second wavelet decomposition (17) of said values of said Single Ion Chromatogram (SIC) to generate a second processed vector (18) representative of said Single Ion Chromatogram (SIC) cleaned of any oscillations generated by stochastic noise (12b);
• setting a threshold value (S);
• processing said first processed vector (16) and said second processed vector (18), the latter accounting for said threshold value (S), to generate a third processed vector (19) identifying the baseline value of said Single Ion Chromatogram (SIC) so as to reject the chemical noise.
• wherein it further comprises the step of processing said Single Ion Chromatogram (SIC) and said second (18) and third (19) vectors to generate a filtered vector (20) identifying a value (zi) of said peptide peak (24) below said stochastic and/or chemical noise (12a, 12b).

A system for processing data representative of intensity values of a measurement signal (11), said measurement signal (11) having at least one peptide peak value (24) combined with a stochastic and/or chemical noise (12a, 12b), said system comprising:

• a chromatograph (2) for separating the peptides obtained by enzymatic digestion of the proteins contained in a biological sample;
• a mass spectrometer (3) for detecting spectrum data of said measurement signal (8, 11);
• a computer device for processing the spectrum data of said measurement signal (8, 11), said computer device comprising at least one processor, one memory associated with said at least one processor, a monitor and a computer tool adapted to be loaded in said memory, said computer tool being able for processing data representative of the intensity values of a measurement signal (11), said measurement signal (11) having at least one peak value (24) combined with a stochastic and/or chemical noise (12a, 12b), said computer tool being adapted to be directly loaded into memory of a computer device, comprising portions of program code susceptible of implementing the method when run on said computer device, said method being for noise rejection and detection within the data of a measurement signal (11) generated by the combination of a chromatograph (2) and a mass spectrometer (3), said data identifying the intensity values of the proteins contained in a biological sample, said measurement signal (11) having at least one peak value (24) combined with stochastic and/or chemical noise (12a, 12b), said peak value (24) being representative of a peptide peak that can be found in said measurement signal (11), said method comprising the steps of:
• providing a Single Ion Chromatogram (SIC) representative of the elution values at a specific mass value (m/z) of said measurement signal (11);
• performing a first wavelet decomposition (15) of said values of said Single Ion Chromatogram (SIC) to generate a first processed vector (16) representative of the smoothed intensity values of the Single Ion Chromatogram (SIC);
• performing a second wavelet decomposition (17) of said values of said Single Ion Chromatogram (SIC) to generate a second processed vector (18) representative of said Single Ion Chromatogram (SIC) cleaned of any oscillations generated by stochastic noise (12b);
• setting a threshold value (S);
• processing said first processed vector (16) and said second processed vector (18), the latter accounting for said threshold value (S), to generate a third processed vector (19) identifying the baseline value of said Single Ion Chromatogram (SIC) so as to reject the chemical noise.
• wherein it further comprises the step of processing said Single Ion Chromatogram (SIC) and said second (18) and third (19) vectors to generate a filtered vector (20) identifying a value (zi) of said peptide peak (24) below said stochastic and/or chemical noise (12a, 12b).