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Title: Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues

Journal Article · · Journal of Proteome Research
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  1. Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, United States
  2. Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
  3. Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, Maryland 20892, United States
  4. Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States
  5. Department of Biomedical Informatics, Vanderbilt University Medical School, Nashville, Tennessee 37232, United States
  6. The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
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The identification of protein biomarkers requires large-scale analysis of human specimens to achieve statistical significance. In this study, we evaluated the long-term reproducibility of an iTRAQ (isobaric tags for relative and absolute quantification) based quantitative proteomics strategy using one channel for universal normalization across all samples. A total of 307 liquid chromatography tandem mass spectrometric (LC-MS/MS) analyses were completed, generating 107 one-dimensional (1D) LC-MS/MS datasets and 8 offline two-dimensional (2D) LC-MS/MS datasets (25 fractions for each set) for human-in-mouse breast cancer xenograft tissues representative of basal and luminal subtypes. Such large-scale studies require the implementation of robust metrics to assess the contributions of technical and biological variability in the qualitative and quantitative data. Accordingly, we developed a quantification confidence score based on the quality of each peptide-spectrum match (PSM) to remove quantification outliers from each analysis. After combining confidence score filtering and statistical analysis, reproducible protein identification and quantitative results were achieved from LC-MS/MS datasets collected over a 16 month period.

Research Organization:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Sponsoring Organization:
USDOE
DOE Contract Number:
AC05-76RL01830
OSTI ID:
1414552
Report Number(s):
PNNL-SA-105677; 50062; 453040220
Journal Information:
Journal of Proteome Research, Vol. 16, Issue 12; ISSN 1535-3893
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English

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