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Title: Residual tissue repositories as a resource for population-based cancer proteomic studies

Abstract

Mass spectrometry-based proteomics has become a powerful tool for the identification and quantification of proteins from a wide variety of biological specimens. To date, the majority of studies utilizing tissue samples have been carried out on fresh frozen or Optimal Cutting Temperature (OCT) embedded specimens. However, these specimens are often in limited supply and lack prospective patient information. Thus, the available archived formalin fixed, paraffin embedded (FFPE) tissue blocks from the Surveillance, Epidemiology and End Results (SEER) registries’ Residual Tissue Repositories represent a significant potential resource for population-based cancer studies. To examine the suitability of these tissues for proteomic and phosphoproteomic analysis, we analyzed 60 SEER patient samples, with time in storage ranging from 7 to 32 years; 60 samples with global proteomics and 18 with phosphoproteomics using isobaric labeling. All samples, regardless of age, yielded suitable protein mass after extraction for global analysis and 18 samples yielded sufficient mass for phosphopeptide analysis. Although fewer protein and phosphopeptide identifications were made than from similar OCT specimens, we found no statistically significant differences in protein quality or quantity correlating with collection site or specimen age. These studies demonstrate that residual FFPE tissue specimens, of varying age and collection site, are amore » promising source of protein for global proteomic investigations with some caveats.« less

Authors:
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Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1503586
Report Number(s):
PNNL-SA-130920
Journal ID: ISSN 1542-6416
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Clinical Proteomics
Additional Journal Information:
Journal Volume: 15; Journal Issue: 1; Journal ID: ISSN 1542-6416
Country of Publication:
United States
Language:
English

Citation Formats

Piehowski, Paul D., Petyuk, Vladislav A., Sontag, Ryan L., Gritsenko, Marina A., Weitz, Karl K., Fillmore, Thomas L., Moon, Jamie, Makhlouf, Hala, Chuaqui, Rodrigo F., Boja, Emily S., Rodriguez, Henry, Lee, Jerry S. H., Smith, Richard D., Carrick, Danielle M., Liu, Tao, and Rodland, Karin D. Residual tissue repositories as a resource for population-based cancer proteomic studies. United States: N. p., 2018. Web. doi:10.1186/s12014-018-9202-4.
Piehowski, Paul D., Petyuk, Vladislav A., Sontag, Ryan L., Gritsenko, Marina A., Weitz, Karl K., Fillmore, Thomas L., Moon, Jamie, Makhlouf, Hala, Chuaqui, Rodrigo F., Boja, Emily S., Rodriguez, Henry, Lee, Jerry S. H., Smith, Richard D., Carrick, Danielle M., Liu, Tao, & Rodland, Karin D. Residual tissue repositories as a resource for population-based cancer proteomic studies. United States. doi:10.1186/s12014-018-9202-4.
Piehowski, Paul D., Petyuk, Vladislav A., Sontag, Ryan L., Gritsenko, Marina A., Weitz, Karl K., Fillmore, Thomas L., Moon, Jamie, Makhlouf, Hala, Chuaqui, Rodrigo F., Boja, Emily S., Rodriguez, Henry, Lee, Jerry S. H., Smith, Richard D., Carrick, Danielle M., Liu, Tao, and Rodland, Karin D. Fri . "Residual tissue repositories as a resource for population-based cancer proteomic studies". United States. doi:10.1186/s12014-018-9202-4.
@article{osti_1503586,
title = {Residual tissue repositories as a resource for population-based cancer proteomic studies},
author = {Piehowski, Paul D. and Petyuk, Vladislav A. and Sontag, Ryan L. and Gritsenko, Marina A. and Weitz, Karl K. and Fillmore, Thomas L. and Moon, Jamie and Makhlouf, Hala and Chuaqui, Rodrigo F. and Boja, Emily S. and Rodriguez, Henry and Lee, Jerry S. H. and Smith, Richard D. and Carrick, Danielle M. and Liu, Tao and Rodland, Karin D.},
abstractNote = {Mass spectrometry-based proteomics has become a powerful tool for the identification and quantification of proteins from a wide variety of biological specimens. To date, the majority of studies utilizing tissue samples have been carried out on fresh frozen or Optimal Cutting Temperature (OCT) embedded specimens. However, these specimens are often in limited supply and lack prospective patient information. Thus, the available archived formalin fixed, paraffin embedded (FFPE) tissue blocks from the Surveillance, Epidemiology and End Results (SEER) registries’ Residual Tissue Repositories represent a significant potential resource for population-based cancer studies. To examine the suitability of these tissues for proteomic and phosphoproteomic analysis, we analyzed 60 SEER patient samples, with time in storage ranging from 7 to 32 years; 60 samples with global proteomics and 18 with phosphoproteomics using isobaric labeling. All samples, regardless of age, yielded suitable protein mass after extraction for global analysis and 18 samples yielded sufficient mass for phosphopeptide analysis. Although fewer protein and phosphopeptide identifications were made than from similar OCT specimens, we found no statistically significant differences in protein quality or quantity correlating with collection site or specimen age. These studies demonstrate that residual FFPE tissue specimens, of varying age and collection site, are a promising source of protein for global proteomic investigations with some caveats.},
doi = {10.1186/s12014-018-9202-4},
journal = {Clinical Proteomics},
issn = {1542-6416},
number = 1,
volume = 15,
place = {United States},
year = {2018},
month = {8}
}