Stability and reproducibility of proteomic profiles in epidemiological studies: comparing the Olink and SOMAscan platforms
Limited data exist on the performance of high‐throughput proteomics profiling in epidemiological settings, including the impact of specimen collection and within‐person variability over time. Thus, the Olink (972 proteins) and SOMAscan7Kv4.1 (7322 proteoforms of 6596 proteins) assays were utilized t...
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| Veröffentlicht in: | Proteomics (Weinheim) 2022-07, Vol.22 (13-14), p.e2100170-n/a |
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| creator | Haslam, Danielle E. Li, Jun Dillon, Simon T. Gu, Xuesong Cao, Yin Zeleznik, Oana A. Sasamoto, Naoko Zhang, Xuehong Eliassen, A. Heather Liang, Liming Stampfer, Meir J. Mora, Samia Chen, Zsu‐Zsu Terry, Kathryn L. Gerszten, Robert E. Hu, Frank B. Chan, Andrew T. Libermann, Towia A. Bhupathiraju, Shilpa N. |
| description | Limited data exist on the performance of high‐throughput proteomics profiling in epidemiological settings, including the impact of specimen collection and within‐person variability over time. Thus, the Olink (972 proteins) and SOMAscan7Kv4.1 (7322 proteoforms of 6596 proteins) assays were utilized to measure protein concentrations in archived plasma samples from the Nurses’ Health Studies and Health Professionals Follow‐Up Study. Spearman's correlation coefficients (r) and intraclass correlation coefficients (ICCs) were used to assess agreement between (1) 42 triplicate samples processed immediately, 24‐h or 48‐h after blood collection from 14 participants; and (2) 80 plasma samples from 40 participants collected 1‐year apart. When comparing samples processed immediately, 24‐h, and 48‐h later, 55% of assays had an ICC/r ≥ 0.75 and 87% had an ICC/r ≥ 0.40 in Olink compared to 44% with an ICC/r ≥ 0.75 and 72% with an ICC/r ≥ 0.40 in SOMAscan7K. For both platforms, >90% of the assays were stable (ICC/r ≥ 0.40) in samples collected 1‐year apart. Among 817 proteins measured with both platforms, Spearman's correlations were high (r > 0.75) for 14.7% and poor (r |
| doi_str_mv | 10.1002/pmic.202100170 |
| format | Article |
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Heather ; Liang, Liming ; Stampfer, Meir J. ; Mora, Samia ; Chen, Zsu‐Zsu ; Terry, Kathryn L. ; Gerszten, Robert E. ; Hu, Frank B. ; Chan, Andrew T. ; Libermann, Towia A. ; Bhupathiraju, Shilpa N.</creator><creatorcontrib>Haslam, Danielle E. ; Li, Jun ; Dillon, Simon T. ; Gu, Xuesong ; Cao, Yin ; Zeleznik, Oana A. ; Sasamoto, Naoko ; Zhang, Xuehong ; Eliassen, A. Heather ; Liang, Liming ; Stampfer, Meir J. ; Mora, Samia ; Chen, Zsu‐Zsu ; Terry, Kathryn L. ; Gerszten, Robert E. ; Hu, Frank B. ; Chan, Andrew T. ; Libermann, Towia A. ; Bhupathiraju, Shilpa N.</creatorcontrib><description>Limited data exist on the performance of high‐throughput proteomics profiling in epidemiological settings, including the impact of specimen collection and within‐person variability over time. Thus, the Olink (972 proteins) and SOMAscan7Kv4.1 (7322 proteoforms of 6596 proteins) assays were utilized to measure protein concentrations in archived plasma samples from the Nurses’ Health Studies and Health Professionals Follow‐Up Study. Spearman's correlation coefficients (r) and intraclass correlation coefficients (ICCs) were used to assess agreement between (1) 42 triplicate samples processed immediately, 24‐h or 48‐h after blood collection from 14 participants; and (2) 80 plasma samples from 40 participants collected 1‐year apart. When comparing samples processed immediately, 24‐h, and 48‐h later, 55% of assays had an ICC/r ≥ 0.75 and 87% had an ICC/r ≥ 0.40 in Olink compared to 44% with an ICC/r ≥ 0.75 and 72% with an ICC/r ≥ 0.40 in SOMAscan7K. For both platforms, >90% of the assays were stable (ICC/r ≥ 0.40) in samples collected 1‐year apart. Among 817 proteins measured with both platforms, Spearman's correlations were high (r > 0.75) for 14.7% and poor (r < 0.40) for 44.8% of proteins. High‐throughput proteomics profiling demonstrated reproducibility in archived plasma samples and stability after delayed processing in epidemiological studies, yet correlations between proteins measured with the Olink and SOMAscan7K platforms were highly variable.</description><identifier>ISSN: 1615-9853</identifier><identifier>EISSN: 1615-9861</identifier><identifier>DOI: 10.1002/pmic.202100170</identifier><identifier>PMID: 35598103</identifier><language>eng</language><publisher>Germany: Wiley Subscription Services, Inc</publisher><subject>Aptamers ; Assaying ; biomarkers ; Correlation coefficient ; Correlation coefficients ; Epidemiologic Studies ; Epidemiology ; epidemiology studies ; Follow-Up Studies ; Humans ; laboratory methods and tools ; Medical personnel ; multiplexing ; Platforms ; Proteins ; Proteomics ; Reproducibility ; Reproducibility of Results ; Specimen Handling ; Stability ; systems biology</subject><ispartof>Proteomics (Weinheim), 2022-07, Vol.22 (13-14), p.e2100170-n/a</ispartof><rights>2022 Wiley‐VCH GmbH.</rights><rights>2022 Wiley-VCH GmbH.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4649-d11ec92798129eb6d9303b916c42146368cfd7b3dbefcb32e507ba4407ce46e23</citedby><cites>FETCH-LOGICAL-c4649-d11ec92798129eb6d9303b916c42146368cfd7b3dbefcb32e507ba4407ce46e23</cites><orcidid>0000-0003-0144-3287</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fpmic.202100170$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fpmic.202100170$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,314,776,780,881,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35598103$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Haslam, Danielle E.</creatorcontrib><creatorcontrib>Li, Jun</creatorcontrib><creatorcontrib>Dillon, Simon T.</creatorcontrib><creatorcontrib>Gu, Xuesong</creatorcontrib><creatorcontrib>Cao, Yin</creatorcontrib><creatorcontrib>Zeleznik, Oana A.</creatorcontrib><creatorcontrib>Sasamoto, Naoko</creatorcontrib><creatorcontrib>Zhang, Xuehong</creatorcontrib><creatorcontrib>Eliassen, A. Heather</creatorcontrib><creatorcontrib>Liang, Liming</creatorcontrib><creatorcontrib>Stampfer, Meir J.</creatorcontrib><creatorcontrib>Mora, Samia</creatorcontrib><creatorcontrib>Chen, Zsu‐Zsu</creatorcontrib><creatorcontrib>Terry, Kathryn L.</creatorcontrib><creatorcontrib>Gerszten, Robert E.</creatorcontrib><creatorcontrib>Hu, Frank B.</creatorcontrib><creatorcontrib>Chan, Andrew T.</creatorcontrib><creatorcontrib>Libermann, Towia A.</creatorcontrib><creatorcontrib>Bhupathiraju, Shilpa N.</creatorcontrib><title>Stability and reproducibility of proteomic profiles in epidemiological studies: comparing the Olink and SOMAscan platforms</title><title>Proteomics (Weinheim)</title><addtitle>Proteomics</addtitle><description>Limited data exist on the performance of high‐throughput proteomics profiling in epidemiological settings, including the impact of specimen collection and within‐person variability over time. Thus, the Olink (972 proteins) and SOMAscan7Kv4.1 (7322 proteoforms of 6596 proteins) assays were utilized to measure protein concentrations in archived plasma samples from the Nurses’ Health Studies and Health Professionals Follow‐Up Study. Spearman's correlation coefficients (r) and intraclass correlation coefficients (ICCs) were used to assess agreement between (1) 42 triplicate samples processed immediately, 24‐h or 48‐h after blood collection from 14 participants; and (2) 80 plasma samples from 40 participants collected 1‐year apart. When comparing samples processed immediately, 24‐h, and 48‐h later, 55% of assays had an ICC/r ≥ 0.75 and 87% had an ICC/r ≥ 0.40 in Olink compared to 44% with an ICC/r ≥ 0.75 and 72% with an ICC/r ≥ 0.40 in SOMAscan7K. For both platforms, >90% of the assays were stable (ICC/r ≥ 0.40) in samples collected 1‐year apart. Among 817 proteins measured with both platforms, Spearman's correlations were high (r > 0.75) for 14.7% and poor (r < 0.40) for 44.8% of proteins. High‐throughput proteomics profiling demonstrated reproducibility in archived plasma samples and stability after delayed processing in epidemiological studies, yet correlations between proteins measured with the Olink and SOMAscan7K platforms were highly variable.</description><subject>Aptamers</subject><subject>Assaying</subject><subject>biomarkers</subject><subject>Correlation coefficient</subject><subject>Correlation coefficients</subject><subject>Epidemiologic Studies</subject><subject>Epidemiology</subject><subject>epidemiology studies</subject><subject>Follow-Up Studies</subject><subject>Humans</subject><subject>laboratory methods and tools</subject><subject>Medical personnel</subject><subject>multiplexing</subject><subject>Platforms</subject><subject>Proteins</subject><subject>Proteomics</subject><subject>Reproducibility</subject><subject>Reproducibility of Results</subject><subject>Specimen Handling</subject><subject>Stability</subject><subject>systems biology</subject><issn>1615-9853</issn><issn>1615-9861</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU1v1DAQhiNERT_gyhFZ4tLLLv5I7JgDUrVqoVKrRSqcLceebF2cONgJaPvrcdhlRblw8njm8TszfoviNcFLgjF9N3TOLCmm-UIEflacEE6qhaw5eX6IK3ZcnKb0MCO1FC-KY1ZVsiaYnRSPd6NunHfjFuneoghDDHYybp8LLcqJEUJuM0et85CQ6xEMzkLngg8bZ7RHaZysg_QemdANOrp-g8Z7QGvv-m-_le_WtxfJ6B4NXo9tiF16WRy12id4tT_Piq9Xl19WnxY364_Xq4ubhSl5KReWEDCSijwwldBwKxlmjSTclJSUnPHatFY0zDbQmoZRqLBodFliYaDkQNlZ8WGnO0xNB9ZAP0bt1RBdp-NWBe3U00rv7tUm_FBSUiYEzgLne4EYvk-QRtW5ZMB73UOYkqKcC1ELUs293v6DPoQp9nm9TNWCy_zvIlPLHWViSClCexiGYDXbqmZb1cHW_ODN3ysc8D8-ZqDaAT-zQdv_yKnPt9crwioq2S8xoLE-</recordid><startdate>202207</startdate><enddate>202207</enddate><creator>Haslam, Danielle E.</creator><creator>Li, Jun</creator><creator>Dillon, Simon T.</creator><creator>Gu, Xuesong</creator><creator>Cao, Yin</creator><creator>Zeleznik, Oana A.</creator><creator>Sasamoto, Naoko</creator><creator>Zhang, Xuehong</creator><creator>Eliassen, A. Heather</creator><creator>Liang, Liming</creator><creator>Stampfer, Meir J.</creator><creator>Mora, Samia</creator><creator>Chen, Zsu‐Zsu</creator><creator>Terry, Kathryn L.</creator><creator>Gerszten, Robert E.</creator><creator>Hu, Frank B.</creator><creator>Chan, Andrew T.</creator><creator>Libermann, Towia A.</creator><creator>Bhupathiraju, Shilpa N.</creator><general>Wiley Subscription Services, Inc</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>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-0144-3287</orcidid></search><sort><creationdate>202207</creationdate><title>Stability and reproducibility of proteomic profiles in epidemiological studies: comparing the Olink and SOMAscan platforms</title><author>Haslam, Danielle E. ; Li, Jun ; Dillon, Simon T. ; Gu, Xuesong ; Cao, Yin ; Zeleznik, Oana A. ; Sasamoto, Naoko ; Zhang, Xuehong ; Eliassen, A. 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Heather</au><au>Liang, Liming</au><au>Stampfer, Meir J.</au><au>Mora, Samia</au><au>Chen, Zsu‐Zsu</au><au>Terry, Kathryn L.</au><au>Gerszten, Robert E.</au><au>Hu, Frank B.</au><au>Chan, Andrew T.</au><au>Libermann, Towia A.</au><au>Bhupathiraju, Shilpa N.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Stability and reproducibility of proteomic profiles in epidemiological studies: comparing the Olink and SOMAscan platforms</atitle><jtitle>Proteomics (Weinheim)</jtitle><addtitle>Proteomics</addtitle><date>2022-07</date><risdate>2022</risdate><volume>22</volume><issue>13-14</issue><spage>e2100170</spage><epage>n/a</epage><pages>e2100170-n/a</pages><issn>1615-9853</issn><eissn>1615-9861</eissn><abstract>Limited data exist on the performance of high‐throughput proteomics profiling in epidemiological settings, including the impact of specimen collection and within‐person variability over time. 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| subjects | Aptamers Assaying biomarkers Correlation coefficient Correlation coefficients Epidemiologic Studies Epidemiology epidemiology studies Follow-Up Studies Humans laboratory methods and tools Medical personnel multiplexing Platforms Proteins Proteomics Reproducibility Reproducibility of Results Specimen Handling Stability systems biology |
| title | Stability and reproducibility of proteomic profiles in epidemiological studies: comparing the Olink and SOMAscan platforms |
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