EVALUATING DYNAMIC RANGE AND PEAK CAPACITY IN MASS SPECTROMETRY EXPERIMENTS

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The value of mass spectrometry experiments is often assessed by the quantity and quality of results, especially in proteomics experiments where the information obtained (i.e., protein identifications) is often two or more steps removed from the raw data from which it is derived. The quality of an analysis can, however, be examined prior to the lengthy postprocessing steps required to arrive at that identification (e.g. SEQUEST processing), by examining attributes of the raw data. Critical but seldom-assessed measures of the quality of mass spectrometry experiments include general measures of data quality such as dynamic range, peak capacity, and the number of detected signals of interest. We are developing software to assess these quantities globally for each data set generated on our mass spectrometers. The software takes mass spectrometry data files in the MS1 and MS2 formats as inputs and: (1) counts the number of signals detected, where a "signal" is defined as a peak found and persisting across a large percentage of consecutive mass scans within user- specified windows of retention time and m/z units and above a user-specified signal-to-noise level; (2) computes the dynamic range, defined as the intensity of the most intense detected signal in the entire dataset divided by the intensity of the least intense detected signal; and (3) computes the peak capacity in each dimension of peptide separation by computing the width of the peaks and dividing the range over which measurements are made by this width. Output of the software consists of (1) a summary file in which dynamic range and peak capacity measurements, as well as other data attributes like number of spectra, are reported; (2) a filtered data file in MS1/MS2 format consisting only of the signals detected.