Abstract
Accurate and precise measurement of the relative protein content of blood-based samples using mass spectrometry is challenging due to the large number of circulating proteins and the dynamic range of their abundances. Traditional spectral processing methods often struggle with accurately detecting overlapping peaks that are observed in these samples. In this work, we develop a novel spectral processing algorithm that effectively detects over 1650 peaks with over 3.5 orders of magnitude in intensity in the 3 to 30 kD m/z range. The algorithm utilizes a convolution of the peak shape to enhance peak detection, and accurate peak fitting to provide highly reproducible relative abundance estimates for both isolated peaks and overlapping peaks. We demonstrate a substantial increase in the reproducibility of the measurements of relative protein abundance when comparing this processing method to a traditional processing method for sample sets run on multiple matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) instruments. By utilizing protein set enrichment analysis, we find a sizable increase in the number of features associated with biological processes compared to previously reported results. The new processing method could be very beneficial when developing high-performance molecular diagnostic tests in disease indications.
Highlights
Protein abundance in blood is related to outcomes in many systemic diseases and cancer
Such diagnostic tests have been developed based on highly sensitive high-throughput matrix-assisted laser desorption/ionization (MALDI) profiling, Deep MALDI® [6] analysis, which enables the simultaneous measurement of proteins varying in abundance by four orders of magnitude
We developed a novel method for analyzing MALDI-TOF spectra over a wide spectral range
Summary
Protein abundance in blood is related to outcomes in many systemic diseases and cancer. Due to the complexity of pathway interactions, it is likely that a multiplexed measurement of many proteins will allow for more accurate characterization of a patient cohort in a particular disease Such diagnostic tests have been developed based on highly sensitive high-throughput matrix-assisted laser desorption/ionization (MALDI) profiling, Deep MALDI® [6] analysis, which enables the simultaneous measurement of proteins varying in abundance by four orders of magnitude. The stiff background does not overfit the spectra and subtraction from the spectra results in sharp features that still are sitting on top of broad features, as seen in Figures 2 and 4 Both the bumps and the sharp peaks may contain useful information as to total protein content in the sample but need to be treated separately to ensure accurate estimation of feature values. The bumps were defined as the difference between the aggressive background and the stiff background
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