MS/MS Interpretation

Probability Assignment

Protein Quantification


Curation of Protein IDs




data repository



This project is hosted at


Protein quantification


The XPRESS software calculates the relative abundance of proteins, such as those obtained from an ICAT-reagent labeled experiment, by reconstructing the light and heavy elution profiles of the precursor ions and determining the elution areas of each peak. The software allows the specification of which residue(s) are labeled (such as cysteines for ICAT) and what the mass difference of the two isotope labels are (such as 8 Da for ICAT). There's a built in interface to the INTERACT program that allows for querying/sorting based on the expression values. Averages plus standard deviations are calculated for each protein expression value when multiple peptide measurements are available. The INTERACT interface will also display the average and median XPRESS ratio present in a dataset and correct the protein expression averages by these average and median ratio (for those cases where a systematic expression bias is present). Users are able to view the areas of integration that the software chose and adjust them as needed ... corrected expression values are then updated in the INTERACT list. For those SEQUEST users interested in using the software, ThermoFinnigan has an implementation of XPRESS in their BioWorks package.
Please see the XPRESS page on the SPC Tools wiki for more information, including download instructions.

Reference: "Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry", D.K. Han, J. Eng, H. Zhou, and R. Aebersold, Nature Biotechnology, 19(10), 946-951, 10/2001


Another software tool for relative quantitation of isotopicaly labeled peptide.
Please see the ASAPRatio page on the SPC Tools wiki for more information, including download instructions.

Reference: "Automated Statistical Analysis of Protein Abundance Ratios from Data Generated by Stable-Isotope Dilution and Tandem Mass Spectrometry", Li XJ, Zhang H, Ranish JA, Aebersold R, Analytical Chemistsry, 75(23), 6648-6657 (2003).