LC/MS-based quantitative proteomic analysis of paraffin-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis

Sharon K. Huang, Marlene M. Darfler, Michael B. Nicholl, Jinsam You, Kerry G. Bemis, Tony J. Tegeler, Mu Wang, Jen Pierre Wery, Kelly K. Chong, Linhda Nguyen, Richard A. Scolyer, Dave S B Hoon

Research output: Contribution to journalArticle

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Abstract

Background: Melanoma metastasis status is highly associated with the overall survival of patients; yet, little is known about proteomic changes during melanoma tumor progression. To better understand the changes in protein expression involved in melanoma progression and metastasis, and to identify potential biomarkers, we conducted a global quantitative proteomic analysis on archival metastatic and primary melanomas. Methodology and Findings: A total of 16 metastatic and 8 primary cutaneous melanomas were assessed. Proteins were extracted from laser captured microdissected formalin fixed paraffin-embedded archival tissues by liquefying tissue cells. These preparations were analyzed by a LC/MS-based label-free protein quantification method. More than 1500 proteins were identified in the tissue lysates with a peptide ID confidence level of >75%. This approach identified 120 significant changes in protein levels. These proteins were identified from multiple peptides with high confidence identification and were expressed at significantly different levels in metastases as compared with primary melanomas (q-Value

Original languageEnglish (US)
Article numbere4430
JournalPLoS One
Volume4
Issue number2
DOIs
StatePublished - Feb 16 2009
Externally publishedYes

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Biomarkers
melanoma
metastasis
Paraffin
Proteomics
proteomics
alkanes
Melanoma
biomarkers
Neoplasm Metastasis
Proteins
Tissue
proteins
peptides
Peptides
formalin
Formaldehyde
lasers
Labels
Tumors

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

LC/MS-based quantitative proteomic analysis of paraffin-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis. / Huang, Sharon K.; Darfler, Marlene M.; Nicholl, Michael B.; You, Jinsam; Bemis, Kerry G.; Tegeler, Tony J.; Wang, Mu; Wery, Jen Pierre; Chong, Kelly K.; Nguyen, Linhda; Scolyer, Richard A.; Hoon, Dave S B.

In: PLoS One, Vol. 4, No. 2, e4430, 16.02.2009.

Research output: Contribution to journalArticle

Huang, SK, Darfler, MM, Nicholl, MB, You, J, Bemis, KG, Tegeler, TJ, Wang, M, Wery, JP, Chong, KK, Nguyen, L, Scolyer, RA & Hoon, DSB 2009, 'LC/MS-based quantitative proteomic analysis of paraffin-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis', PLoS One, vol. 4, no. 2, e4430. https://doi.org/10.1371/journal.pone.0004430
Huang, Sharon K. ; Darfler, Marlene M. ; Nicholl, Michael B. ; You, Jinsam ; Bemis, Kerry G. ; Tegeler, Tony J. ; Wang, Mu ; Wery, Jen Pierre ; Chong, Kelly K. ; Nguyen, Linhda ; Scolyer, Richard A. ; Hoon, Dave S B. / LC/MS-based quantitative proteomic analysis of paraffin-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis. In: PLoS One. 2009 ; Vol. 4, No. 2.
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abstract = "Background: Melanoma metastasis status is highly associated with the overall survival of patients; yet, little is known about proteomic changes during melanoma tumor progression. To better understand the changes in protein expression involved in melanoma progression and metastasis, and to identify potential biomarkers, we conducted a global quantitative proteomic analysis on archival metastatic and primary melanomas. Methodology and Findings: A total of 16 metastatic and 8 primary cutaneous melanomas were assessed. Proteins were extracted from laser captured microdissected formalin fixed paraffin-embedded archival tissues by liquefying tissue cells. These preparations were analyzed by a LC/MS-based label-free protein quantification method. More than 1500 proteins were identified in the tissue lysates with a peptide ID confidence level of >75{\%}. This approach identified 120 significant changes in protein levels. These proteins were identified from multiple peptides with high confidence identification and were expressed at significantly different levels in metastases as compared with primary melanomas (q-Value",
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AU - Huang, Sharon K.

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AU - Nicholl, Michael B.

AU - You, Jinsam

AU - Bemis, Kerry G.

AU - Tegeler, Tony J.

AU - Wang, Mu

AU - Wery, Jen Pierre

AU - Chong, Kelly K.

AU - Nguyen, Linhda

AU - Scolyer, Richard A.

AU - Hoon, Dave S B

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AB - Background: Melanoma metastasis status is highly associated with the overall survival of patients; yet, little is known about proteomic changes during melanoma tumor progression. To better understand the changes in protein expression involved in melanoma progression and metastasis, and to identify potential biomarkers, we conducted a global quantitative proteomic analysis on archival metastatic and primary melanomas. Methodology and Findings: A total of 16 metastatic and 8 primary cutaneous melanomas were assessed. Proteins were extracted from laser captured microdissected formalin fixed paraffin-embedded archival tissues by liquefying tissue cells. These preparations were analyzed by a LC/MS-based label-free protein quantification method. More than 1500 proteins were identified in the tissue lysates with a peptide ID confidence level of >75%. This approach identified 120 significant changes in protein levels. These proteins were identified from multiple peptides with high confidence identification and were expressed at significantly different levels in metastases as compared with primary melanomas (q-Value

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