High-throughput mass spectrometry data from shotgun proteomics experiments necessitate an efficient and automated way to analyze large amounts of quantitative data. We introduce a software tool called Census that facilitates automated quantitative analysis using either stable isotope labeling or an isotope free strategy. Using high-resolution and high mass accuracy data from an LTQ-Orbitrap hybrid mass spectrometer as input for Census, we were able to quantify roughly three times as many peptides as our previous software (i.e., RelEx). While some of the increase can be attributed to the benefits inherent to the instrumentation, improvements in Census are also responsible. One of the reasons for the increase in accurately quantified peptides is that Census minimizes the contributions of interfering peaks and chemical noise by taking advantage of the high mass accuracy of the Orbitrap using a small mass accuracy tolerance for each isotopic peak. In addition, a dynamic peak finding algorithm is employed that makes use of database search results for improved accuracy and quantification efficiency. Finally, a weighted means of the peptides are calculated to determine the protein ratios.
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