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Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer

BACKGROUND: Serum is an ideal source of biomarker discovery and proteomic profiling studies are continuously pursued on serum samples. However, serum is featured by high level of protein glycosylations that often cause ionization suppression and confound accurate quantification analysis by mass spec...

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Autores principales: Toyama, Atsuhiko, Nakagawa, Hidewaki, Matsuda, Koichi, Ishikawa, Nobuhisa, Kohno, Nobuoki, Daigo, Yataro, Sato, Taka-Aki, Nakamura, Yusuke, Ueda, Koji
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090313/
https://www.ncbi.nlm.nih.gov/pubmed/21473792
http://dx.doi.org/10.1186/1477-5956-9-18
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author Toyama, Atsuhiko
Nakagawa, Hidewaki
Matsuda, Koichi
Ishikawa, Nobuhisa
Kohno, Nobuoki
Daigo, Yataro
Sato, Taka-Aki
Nakamura, Yusuke
Ueda, Koji
author_facet Toyama, Atsuhiko
Nakagawa, Hidewaki
Matsuda, Koichi
Ishikawa, Nobuhisa
Kohno, Nobuoki
Daigo, Yataro
Sato, Taka-Aki
Nakamura, Yusuke
Ueda, Koji
author_sort Toyama, Atsuhiko
collection PubMed
description BACKGROUND: Serum is an ideal source of biomarker discovery and proteomic profiling studies are continuously pursued on serum samples. However, serum is featured by high level of protein glycosylations that often cause ionization suppression and confound accurate quantification analysis by mass spectrometry. Here we investigated the effect of N-glycan and sialic acid removal from serum proteins on the performance of label-free quantification results. RESULTS: Serum tryptic digests with or without deglycosylation treatment were analyzed by LC-MALDI MS and quantitatively compared on the Expressionist Refiner MS module. As a result, 345 out of 2,984 peaks (11.6%) showed the specific detection or the significantly improved intensities in deglycosylated serum samples (P < 0.01). We then applied this deglycosylation-based sample preparation to the identification of lung cancer biomarkers. In comparison between 10 healthy controls and 20 lung cancer patients, 40 peptides were identified to be differentially presented (P < 0.01). Their quantitative accuracies were further verified by multiple reaction monitoring. The result showed that deglycosylation was needed for the identification of some unique candidates, including previously unreported O-linked glycopeptide of complement component C9. CONCLUSIONS: We demonstrated here that sample deglycosylation improves the quantitative performance of shotgun proteomics, which can be effectively applied to any samples with high glycoprotein contents.
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spelling pubmed-30903132011-05-10 Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer Toyama, Atsuhiko Nakagawa, Hidewaki Matsuda, Koichi Ishikawa, Nobuhisa Kohno, Nobuoki Daigo, Yataro Sato, Taka-Aki Nakamura, Yusuke Ueda, Koji Proteome Sci Research BACKGROUND: Serum is an ideal source of biomarker discovery and proteomic profiling studies are continuously pursued on serum samples. However, serum is featured by high level of protein glycosylations that often cause ionization suppression and confound accurate quantification analysis by mass spectrometry. Here we investigated the effect of N-glycan and sialic acid removal from serum proteins on the performance of label-free quantification results. RESULTS: Serum tryptic digests with or without deglycosylation treatment were analyzed by LC-MALDI MS and quantitatively compared on the Expressionist Refiner MS module. As a result, 345 out of 2,984 peaks (11.6%) showed the specific detection or the significantly improved intensities in deglycosylated serum samples (P < 0.01). We then applied this deglycosylation-based sample preparation to the identification of lung cancer biomarkers. In comparison between 10 healthy controls and 20 lung cancer patients, 40 peptides were identified to be differentially presented (P < 0.01). Their quantitative accuracies were further verified by multiple reaction monitoring. The result showed that deglycosylation was needed for the identification of some unique candidates, including previously unreported O-linked glycopeptide of complement component C9. CONCLUSIONS: We demonstrated here that sample deglycosylation improves the quantitative performance of shotgun proteomics, which can be effectively applied to any samples with high glycoprotein contents. BioMed Central 2011-04-08 /pmc/articles/PMC3090313/ /pubmed/21473792 http://dx.doi.org/10.1186/1477-5956-9-18 Text en Copyright ©2011 Toyama et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Toyama, Atsuhiko
Nakagawa, Hidewaki
Matsuda, Koichi
Ishikawa, Nobuhisa
Kohno, Nobuoki
Daigo, Yataro
Sato, Taka-Aki
Nakamura, Yusuke
Ueda, Koji
Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer
title Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer
title_full Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer
title_fullStr Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer
title_full_unstemmed Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer
title_short Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer
title_sort deglycosylation and label-free quantitative lc-maldi ms applied to efficient serum biomarker discovery of lung cancer
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090313/
https://www.ncbi.nlm.nih.gov/pubmed/21473792
http://dx.doi.org/10.1186/1477-5956-9-18
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