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.
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. A full manuscript describing this work is under peer review.
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.
Software packages, providing graphical support, based in some part on these metrics:
You will need the software and a library to run the pipeline. You may also want to test your installation with the test data below.
The package can be downloaded here. 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.
This software was developed by the Chemical Reference Data Group at NIST, led by Steve Stein. The original ReAdW source code was developed by Patrick Pedrioli, and SpectraST was developed by Henry Lam both at the Institute for Systems Biology. OMSSA 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 Institute. 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 Cancer, (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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