A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics
Animals with large adipose stores, such as marine mammals, may provide insights into the evolution and function of this multifunctional tissue in health and disease. In the absence of sequenced genomes, molecular information can be rapidly obtained by proteomics and transcriptomics, but their applic...
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fthighwire:oai:open-archive.highwire.org:biolopen:7/11/bio036731 2023-05-15T16:05:17+02:00 A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics Khudyakov, Jane I. Deyarmin, Jared S. Hekman, Ryan M. Pujade Busqueta, Laura Maan, Rasool Mody, Melony J. Banerjee, Reeti Crocker, Daniel E. Champagne, Cory D. 2018-11-19 03:25:19.0 text/html http://bio.biologists.org/cgi/content/short/7/11/bio036731 https://doi.org/10.1242/bio.036731 en eng The Company of Biologists Ltd http://bio.biologists.org/cgi/content/short/7/11/bio036731 http://dx.doi.org/10.1242/bio.036731 Copyright (C) 2018, Company of Biologists METHODS AND TECHNIQUES TEXT 2018 fthighwire https://doi.org/10.1242/bio.036731 2018-12-30T19:24:28Z Animals with large adipose stores, such as marine mammals, may provide insights into the evolution and function of this multifunctional tissue in health and disease. In the absence of sequenced genomes, molecular information can be rapidly obtained by proteomics and transcriptomics, but their application to adipose tissue is hindered by low nucleic acid and protein yields. We sequenced and compared proteomes isolated from the blubber of four elephant seals using phenol and guanidine thiocyanate (Qiazol) or detergent (sodium deoxycholate) buffer. Qiazol recovered more subcellular proteins such as metabolic enzymes, in addition to extracting RNA, facilitating proteogenomic analyses of small lipid-rich tissue biopsies. We also compared proteomics data analysis platforms and found that de novo peptide sequencing improved protein identification sensitivity compared to database search alone. We report sample preparation and data analysis workflows for proteogenomics and a proteome of elephant seal blubber containing 2678 proteins, including many of interest for further functional studies. This article has an associated First Person interview with the first author of the paper . Text Elephant Seal Elephant Seals HighWire Press (Stanford University) Biology Open |
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METHODS AND TECHNIQUES |
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METHODS AND TECHNIQUES Khudyakov, Jane I. Deyarmin, Jared S. Hekman, Ryan M. Pujade Busqueta, Laura Maan, Rasool Mody, Melony J. Banerjee, Reeti Crocker, Daniel E. Champagne, Cory D. A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics |
topic_facet |
METHODS AND TECHNIQUES |
description |
Animals with large adipose stores, such as marine mammals, may provide insights into the evolution and function of this multifunctional tissue in health and disease. In the absence of sequenced genomes, molecular information can be rapidly obtained by proteomics and transcriptomics, but their application to adipose tissue is hindered by low nucleic acid and protein yields. We sequenced and compared proteomes isolated from the blubber of four elephant seals using phenol and guanidine thiocyanate (Qiazol) or detergent (sodium deoxycholate) buffer. Qiazol recovered more subcellular proteins such as metabolic enzymes, in addition to extracting RNA, facilitating proteogenomic analyses of small lipid-rich tissue biopsies. We also compared proteomics data analysis platforms and found that de novo peptide sequencing improved protein identification sensitivity compared to database search alone. We report sample preparation and data analysis workflows for proteogenomics and a proteome of elephant seal blubber containing 2678 proteins, including many of interest for further functional studies. This article has an associated First Person interview with the first author of the paper . |
format |
Text |
author |
Khudyakov, Jane I. Deyarmin, Jared S. Hekman, Ryan M. Pujade Busqueta, Laura Maan, Rasool Mody, Melony J. Banerjee, Reeti Crocker, Daniel E. Champagne, Cory D. |
author_facet |
Khudyakov, Jane I. Deyarmin, Jared S. Hekman, Ryan M. Pujade Busqueta, Laura Maan, Rasool Mody, Melony J. Banerjee, Reeti Crocker, Daniel E. Champagne, Cory D. |
author_sort |
Khudyakov, Jane I. |
title |
A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics |
title_short |
A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics |
title_full |
A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics |
title_fullStr |
A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics |
title_full_unstemmed |
A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics |
title_sort |
sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics |
publisher |
The Company of Biologists Ltd |
publishDate |
2018 |
url |
http://bio.biologists.org/cgi/content/short/7/11/bio036731 https://doi.org/10.1242/bio.036731 |
genre |
Elephant Seal Elephant Seals |
genre_facet |
Elephant Seal Elephant Seals |
op_relation |
http://bio.biologists.org/cgi/content/short/7/11/bio036731 http://dx.doi.org/10.1242/bio.036731 |
op_rights |
Copyright (C) 2018, Company of Biologists |
op_doi |
https://doi.org/10.1242/bio.036731 |
container_title |
Biology Open |
_version_ |
1766401188925800448 |