A quantitative analysis software tool for mass spectrometry-based proteomics

Abstract

We describe Census, a quantitative software tool compatible with many labeling strategies as well as with label-free analyses, single-stage mass spectrometry (MS1) and tandem mass spectrometry (MS/MS) scans, and high- and low-resolution mass spectrometry data. Census uses robust algorithms to address poor-quality measurements and improve quantitative efficiency, and it can support several input file formats. We tested Census with stable-isotope labeling analyses as well as label-free analyses.

Figure 1

Schematic detailing the quantitative analysis capabilities of Census. (a) shows a schematic of the isotopic labeling strategy and (b) shows our approach to isotope free analysis. These capabilities allows Census to process a wide variety of different types of experimental data including data-independent, SRM and MRM experiments derived from low and high resolution instrumentation utilizing either isotopic labeling or a label free methodology.

Figure 2

Use of high mass accuracy for improved quantification. (a) was generated from LTQ MS scans using the “whole isotopic envelope” method for extraction and (b) was generated from Orbitrap MS scans using the “individual isotope” extraction method and a mass accuracy tolerance of 5 ppm. The green line in the chromatogram represents the identified scan, a close up of which is shown directly above the chromatograms.

Figure 3

Expected and measured relative abundances. They were obtained from the analysis of the 10 protein mix dataset for (a) mixture A over B and (b) mixture A over C using different strategies including LC-MS peak areas, spectral counting without normalization, and spectral counting with normalization. A total of four replicate analyses were performed for each mixture.