NIST LC-MS/MS Metrics for Monitoring Variability in Proteomics Experiments

Goal:

Provide LC-MS/MS users data analysis tools for assessing run-to-run and/or lab-to-lab variability in keys areas of mass spectrometry-based proteomics. Understanding analytical variability and its sources is critical for the confident identification of biomarkers.

Description:

A general overview of this project can be found here. Below, Figure 1, highlights the areas analyzed by the software tool developed here. Each of the metrics has been mapped to a specific area of potential variability and coded for reference.

Intended Use:

This software "pipeline" has been designed to analyze Thermo* .RAW data files from LTQ, FT-LTQ and Orbitrap-LTQ mass spectrometers. Data handling routines for use with other MS vendor-specific formats are under development. This software was written for research purposes ONLY and is provided without support.

Download of the original NIST program and source code is pending publication in Molecular and Cellular Proteomics (in press)

Commercial Implementations*:

Software packages, providing graphical support, based in some part on these metrics:

Figure 2 shows the pipeline and its major components. Processing RAW files requires an installation of XCalibur. The pipeline also requires Perl. Additional peptide mass spectral libraries can be downloaded here.

        Figure 1
        
    
        Figure 2

Credits and Outside Funding Sources:

This software was developed by the Chemical Reference Data Group at NIST, led by Steve Stein. The original ReAdWexternal weblink source code was developed by Patrick Pedrioli, and SpectraSTexternal weblink was developed by Henry Lam both at the Institute for Systems Biology. OMSSAexternal weblink was developed by Lewis Geer at the NCBI.

Portions of this software were developed with funding through an inter-agency agreement with the National Cancer Instituteexternal weblink. The interlaboratory data used to develop this software were generously provided by the principal investigators as part of NCI's Clinical Proteomics Technology Assessment for Cancerexternal weblink, (CPTAC) program.

*Certain commercial equipment, instruments, materials or software are identified in this document. Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the products identified are necessarily the best available for the purpose.

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