LC/MS-based quantitative proteomic analysis of paraffin-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis
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 bio...
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| Veröffentlicht in: | PloS one 2009-02, Vol.4 (2), p.e4430-e4430 |
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| creator | Huang, Sharon K Darfler, Marlene M Nicholl, Michael B You, Jinsam Bemis, Kerry G Tegeler, Tony J Wang, Mu Wery, Jean-Pierre Chong, Kelly K Nguyen, Linhda Scolyer, Richard A Hoon, Dave S B |
| description | 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.
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 |
| doi_str_mv | 10.1371/journal.pone.0004430 |
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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<0.05).
The differentially expressed proteins were classified by biological process or mapped into biological system networks, and several proteins were implicated by these analyses as cancer- or metastasis-related. These proteins represent potential biomarkers for tumor progression. The study successfully identified proteins that are differentially expressed in formalin fixed paraffin-embedded specimens of metastatic and primary melanoma.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0004430</identifier><identifier>PMID: 19221597</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Animals ; Biological activity ; Biological markers ; Biomarkers ; Biomarkers, Tumor - analysis ; Biotechnology/Protein Chemistry and Proteomics ; Cancer ; Cancer metastasis ; Chromatography ; Chromatography, Liquid - methods ; Confidence intervals ; Databases, Protein ; Dehydrogenases ; Formaldehyde ; Gene expression ; Humans ; Hypoxia ; Kinases ; Leukemia ; Liquefaction ; Lysates ; Mass spectrometry ; Mass Spectrometry - methods ; Melanoma ; Melanoma - chemistry ; Melanoma - pathology ; Metabolism ; Metastases ; Metastasis ; Molecular Sequence Data ; Neoplasm Metastasis ; Neoplasm Proteins - analysis ; Oncology ; Oncology/Skin Cancers ; Paraffin ; Paraffin Embedding ; Pathology ; Pathology/Molecular Pathology ; Peptides ; Physiology ; Protein expression ; Proteins ; Proteome - analysis ; Proteomics ; Rodents ; Scientific imaging ; Tissues ; Tumors</subject><ispartof>PloS one, 2009-02, Vol.4 (2), p.e4430-e4430</ispartof><rights>COPYRIGHT 2009 Public Library of Science</rights><rights>2009 Huang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Huang et al. 2009</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c662t-a54f8f681e4954e751662061ac92ff5d14f9d62c50bf93aca30075c0802099d13</citedby><cites>FETCH-LOGICAL-c662t-a54f8f681e4954e751662061ac92ff5d14f9d62c50bf93aca30075c0802099d13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2637971/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2637971/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19221597$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Huang, Sharon K</creatorcontrib><creatorcontrib>Darfler, Marlene M</creatorcontrib><creatorcontrib>Nicholl, Michael B</creatorcontrib><creatorcontrib>You, Jinsam</creatorcontrib><creatorcontrib>Bemis, Kerry G</creatorcontrib><creatorcontrib>Tegeler, Tony J</creatorcontrib><creatorcontrib>Wang, Mu</creatorcontrib><creatorcontrib>Wery, Jean-Pierre</creatorcontrib><creatorcontrib>Chong, Kelly K</creatorcontrib><creatorcontrib>Nguyen, Linhda</creatorcontrib><creatorcontrib>Scolyer, Richard A</creatorcontrib><creatorcontrib>Hoon, Dave S B</creatorcontrib><title>LC/MS-based quantitative proteomic analysis of paraffin-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>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.
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<0.05).
The differentially expressed proteins were classified by biological process or mapped into biological system networks, and several proteins were implicated by these analyses as cancer- or metastasis-related. These proteins represent potential biomarkers for tumor progression. The study successfully identified proteins that are differentially expressed in formalin fixed paraffin-embedded specimens of metastatic and primary melanoma.</description><subject>Analysis</subject><subject>Animals</subject><subject>Biological activity</subject><subject>Biological markers</subject><subject>Biomarkers</subject><subject>Biomarkers, Tumor - analysis</subject><subject>Biotechnology/Protein Chemistry and Proteomics</subject><subject>Cancer</subject><subject>Cancer metastasis</subject><subject>Chromatography</subject><subject>Chromatography, Liquid - methods</subject><subject>Confidence intervals</subject><subject>Databases, Protein</subject><subject>Dehydrogenases</subject><subject>Formaldehyde</subject><subject>Gene expression</subject><subject>Humans</subject><subject>Hypoxia</subject><subject>Kinases</subject><subject>Leukemia</subject><subject>Liquefaction</subject><subject>Lysates</subject><subject>Mass spectrometry</subject><subject>Mass Spectrometry - methods</subject><subject>Melanoma</subject><subject>Melanoma - chemistry</subject><subject>Melanoma - pathology</subject><subject>Metabolism</subject><subject>Metastases</subject><subject>Metastasis</subject><subject>Molecular Sequence Data</subject><subject>Neoplasm Metastasis</subject><subject>Neoplasm Proteins - analysis</subject><subject>Oncology</subject><subject>Oncology/Skin Cancers</subject><subject>Paraffin</subject><subject>Paraffin Embedding</subject><subject>Pathology</subject><subject>Pathology/Molecular Pathology</subject><subject>Peptides</subject><subject>Physiology</subject><subject>Protein expression</subject><subject>Proteins</subject><subject>Proteome - analysis</subject><subject>Proteomics</subject><subject>Rodents</subject><subject>Scientific imaging</subject><subject>Tissues</subject><subject>Tumors</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk99u0zAUxiMEYmPwBggiIU3iop0dO058gzRV_KlUNIkBt9apY7cuaZzZTmEPwvtyuhbWIi5QIiU6_r7fOT72ybLnlIwpq-jFyg-hg3bc-86MCSGcM_IgO6WSFSNREPbw4P8kexLjipCS1UI8zk6oLApayuo0-zmbXHy8Hs0hmia_GaBLLkFyG5P3wSfj107ngGluo4u5t3kPAax13cis56Zp0ARBL90G2nxtWuj8GmIezMZAG_MeCQjEtXvY3KEkfDMh5hCj1w4SQr67tERAgoivi0-zRxYB5tn-e5Z9eff28-TDaHb1fjq5nI20EEUaQcltbUVNDZclN1VJMUwEBS0La8uGcisbUeiSzK1koIERUpWa1KQgUjaUnWUvd9y-9VHtOxoVLWopBS0rhorpTtF4WKk-OCz-Vnlw6i7gw0JBSE63RlnDCitIJTjTHI9IVoRrMGZuiako5ch6s882zNem0dibAO0R9Hilc0u18BtViC1tW-75HhD8zWBiUmsXtWmx78YPUQkhGaN3Vb_6S_jvvY13qgVg-a6zHrNqfBqDJ4XXyjqMX_KKcVLXFUHD6yMDapL5kRYwxKim15_-X3v19Vh7fqBd4t1Jy-jbITnfxWMh3wl18DEGY_80jxK1nYrf-1TbqVD7qUDbi8PG35v2Y8B-AWPpC30</recordid><startdate>20090216</startdate><enddate>20090216</enddate><creator>Huang, Sharon K</creator><creator>Darfler, Marlene M</creator><creator>Nicholl, Michael B</creator><creator>You, Jinsam</creator><creator>Bemis, Kerry G</creator><creator>Tegeler, Tony J</creator><creator>Wang, Mu</creator><creator>Wery, Jean-Pierre</creator><creator>Chong, Kelly K</creator><creator>Nguyen, Linhda</creator><creator>Scolyer, Richard A</creator><creator>Hoon, Dave S B</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20090216</creationdate><title>LC/MS-based quantitative proteomic analysis of paraffin-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis</title><author>Huang, Sharon K ; Darfler, Marlene M ; Nicholl, Michael B ; You, Jinsam ; Bemis, Kerry G ; Tegeler, Tony J ; Wang, Mu ; Wery, Jean-Pierre ; Chong, Kelly K ; Nguyen, Linhda ; Scolyer, Richard A ; Hoon, Dave S B</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c662t-a54f8f681e4954e751662061ac92ff5d14f9d62c50bf93aca30075c0802099d13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Analysis</topic><topic>Animals</topic><topic>Biological activity</topic><topic>Biological markers</topic><topic>Biomarkers</topic><topic>Biomarkers, Tumor - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Huang, Sharon K</au><au>Darfler, Marlene M</au><au>Nicholl, Michael B</au><au>You, Jinsam</au><au>Bemis, Kerry G</au><au>Tegeler, Tony J</au><au>Wang, Mu</au><au>Wery, Jean-Pierre</au><au>Chong, Kelly K</au><au>Nguyen, Linhda</au><au>Scolyer, Richard A</au><au>Hoon, Dave S B</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>LC/MS-based quantitative proteomic analysis of paraffin-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2009-02-16</date><risdate>2009</risdate><volume>4</volume><issue>2</issue><spage>e4430</spage><epage>e4430</epage><pages>e4430-e4430</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>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.
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<0.05).
The differentially expressed proteins were classified by biological process or mapped into biological system networks, and several proteins were implicated by these analyses as cancer- or metastasis-related. These proteins represent potential biomarkers for tumor progression. The study successfully identified proteins that are differentially expressed in formalin fixed paraffin-embedded specimens of metastatic and primary melanoma.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>19221597</pmid><doi>10.1371/journal.pone.0004430</doi><tpages>e4430</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2009-02, Vol.4 (2), p.e4430-e4430 |
| issn | 1932-6203 1932-6203 |
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| source | Electronic Journals Library; Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Animals Biological activity Biological markers Biomarkers Biomarkers, Tumor - analysis Biotechnology/Protein Chemistry and Proteomics Cancer Cancer metastasis Chromatography Chromatography, Liquid - methods Confidence intervals Databases, Protein Dehydrogenases Formaldehyde Gene expression Humans Hypoxia Kinases Leukemia Liquefaction Lysates Mass spectrometry Mass Spectrometry - methods Melanoma Melanoma - chemistry Melanoma - pathology Metabolism Metastases Metastasis Molecular Sequence Data Neoplasm Metastasis Neoplasm Proteins - analysis Oncology Oncology/Skin Cancers Paraffin Paraffin Embedding Pathology Pathology/Molecular Pathology Peptides Physiology Protein expression Proteins Proteome - analysis Proteomics Rodents Scientific imaging Tissues Tumors |
| title | LC/MS-based quantitative proteomic analysis of paraffin-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-01T06%3A52%3A25IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=LC/MS-based%20quantitative%20proteomic%20analysis%20of%20paraffin-embedded%20archival%20melanomas%20reveals%20potential%20proteomic%20biomarkers%20associated%20with%20metastasis&rft.jtitle=PloS%20one&rft.au=Huang,%20Sharon%20K&rft.date=2009-02-16&rft.volume=4&rft.issue=2&rft.spage=e4430&rft.epage=e4430&rft.pages=e4430-e4430&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0004430&rft_dat=%3Cgale_plos_%3EA473408870%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1289961573&rft_id=info:pmid/19221597&rft_galeid=A473408870&rft_doaj_id=oai_doaj_org_article_fe32f607643c41379704caeebf0e7114&rfr_iscdi=true |