Parallel accumulation‐serial fragmentation method for in‐depth proteomic analysis of bronchoalveolar lavage fluid collected from patients with nonsmall cell lung cancer
Purpose Advances in mass spectrometry‐based quantitative proteomic analysis have successfully demonstrated the in‐depth detection of protein biomarkers in bronchoalveolar lavage fluid (BALF) from patients with lung cancers. Recently, ion mobility technology was incorporated into the mass spectromete...
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Veröffentlicht in: | Proteomics. Clinical applications 2024-03, Vol.18 (2), p.e2300053-n/a |
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creator | Vu, Hung M. Huh, Sunghyun Lee, Jun Hyung Lee, Seung Hyeun Kim, Min‐Sik |
description | Purpose
Advances in mass spectrometry‐based quantitative proteomic analysis have successfully demonstrated the in‐depth detection of protein biomarkers in bronchoalveolar lavage fluid (BALF) from patients with lung cancers. Recently, ion mobility technology was incorporated into the mass spectrometers escalating the sensitivity and throughput. Utilizing these advantages, herein, we employed the parallel accumulation–serial fragmentation (PASEF) implanted in a timsTOF Pro mass spectrometer to examine the alteration of BALF proteomes in patients with nonsmall cell lung cancers (NSCLCs).
Experimental design
BALF proteins were processed from patients with NSCLC and analyzed in a timsTOF Pro mass spectrometer with the PASEF method using a peptide input of 100 ng. Label‐free mass spectrometry data were analyzed in the FragPipe platform.
Results
We quantitated over 1400 proteins from a single injection of 100 ng of peptides per sample with a median of ∼2000 proteins. We were able to find a few potential biomarker proteins upregulated in NSCLC.
Conclusions and clinical relevance
The alterations of the BALF proteome landscape vary among patients with NSCLC as previously observed in patients with small‐cell lung cancers. The PASEF method has significantly enhanced the sensitivity and throughput, demonstrating its effectiveness in clinical research and application. |
doi_str_mv | 10.1002/prca.202300053 |
format | Article |
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Advances in mass spectrometry‐based quantitative proteomic analysis have successfully demonstrated the in‐depth detection of protein biomarkers in bronchoalveolar lavage fluid (BALF) from patients with lung cancers. Recently, ion mobility technology was incorporated into the mass spectrometers escalating the sensitivity and throughput. Utilizing these advantages, herein, we employed the parallel accumulation–serial fragmentation (PASEF) implanted in a timsTOF Pro mass spectrometer to examine the alteration of BALF proteomes in patients with nonsmall cell lung cancers (NSCLCs).
Experimental design
BALF proteins were processed from patients with NSCLC and analyzed in a timsTOF Pro mass spectrometer with the PASEF method using a peptide input of 100 ng. Label‐free mass spectrometry data were analyzed in the FragPipe platform.
Results
We quantitated over 1400 proteins from a single injection of 100 ng of peptides per sample with a median of ∼2000 proteins. We were able to find a few potential biomarker proteins upregulated in NSCLC.
Conclusions and clinical relevance
The alterations of the BALF proteome landscape vary among patients with NSCLC as previously observed in patients with small‐cell lung cancers. The PASEF method has significantly enhanced the sensitivity and throughput, demonstrating its effectiveness in clinical research and application.</description><identifier>ISSN: 1862-8346</identifier><identifier>EISSN: 1862-8354</identifier><identifier>DOI: 10.1002/prca.202300053</identifier><identifier>PMID: 38295123</identifier><language>eng</language><publisher>Germany: Wiley Subscription Services, Inc</publisher><subject>Accumulation ; Alveoli ; Biomarkers ; bronchoalveolar lavage fluid ; Bronchus ; Design of experiments ; Fragmentation ; Ionic mobility ; Lavage ; Lung cancer ; Mass spectrometers ; Mass spectrometry ; Mass spectroscopy ; Non-small cell lung carcinoma ; nonsmall cell lung cancer ; PASEF ; Peptides ; Proteins ; Proteomes ; Proteomics ; Scientific imaging ; Sensitivity enhancement</subject><ispartof>Proteomics. Clinical applications, 2024-03, Vol.18 (2), p.e2300053-n/a</ispartof><rights>2024 Wiley‐VCH GmbH.</rights><rights>2024 Wiley-VCH GmbH.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c3237-6f2aa463eef1ef56dac34d80586313c11ea7ece1733aca32942c7cc2188846c73</cites><orcidid>0000-0001-7317-5360</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%2Fprca.202300053$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fprca.202300053$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38295123$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Vu, Hung M.</creatorcontrib><creatorcontrib>Huh, Sunghyun</creatorcontrib><creatorcontrib>Lee, Jun Hyung</creatorcontrib><creatorcontrib>Lee, Seung Hyeun</creatorcontrib><creatorcontrib>Kim, Min‐Sik</creatorcontrib><title>Parallel accumulation‐serial fragmentation method for in‐depth proteomic analysis of bronchoalveolar lavage fluid collected from patients with nonsmall cell lung cancer</title><title>Proteomics. Clinical applications</title><addtitle>Proteomics Clin Appl</addtitle><description>Purpose
Advances in mass spectrometry‐based quantitative proteomic analysis have successfully demonstrated the in‐depth detection of protein biomarkers in bronchoalveolar lavage fluid (BALF) from patients with lung cancers. Recently, ion mobility technology was incorporated into the mass spectrometers escalating the sensitivity and throughput. Utilizing these advantages, herein, we employed the parallel accumulation–serial fragmentation (PASEF) implanted in a timsTOF Pro mass spectrometer to examine the alteration of BALF proteomes in patients with nonsmall cell lung cancers (NSCLCs).
Experimental design
BALF proteins were processed from patients with NSCLC and analyzed in a timsTOF Pro mass spectrometer with the PASEF method using a peptide input of 100 ng. Label‐free mass spectrometry data were analyzed in the FragPipe platform.
Results
We quantitated over 1400 proteins from a single injection of 100 ng of peptides per sample with a median of ∼2000 proteins. We were able to find a few potential biomarker proteins upregulated in NSCLC.
Conclusions and clinical relevance
The alterations of the BALF proteome landscape vary among patients with NSCLC as previously observed in patients with small‐cell lung cancers. The PASEF method has significantly enhanced the sensitivity and throughput, demonstrating its effectiveness in clinical research and application.</description><subject>Accumulation</subject><subject>Alveoli</subject><subject>Biomarkers</subject><subject>bronchoalveolar lavage fluid</subject><subject>Bronchus</subject><subject>Design of experiments</subject><subject>Fragmentation</subject><subject>Ionic mobility</subject><subject>Lavage</subject><subject>Lung cancer</subject><subject>Mass spectrometers</subject><subject>Mass spectrometry</subject><subject>Mass spectroscopy</subject><subject>Non-small cell lung carcinoma</subject><subject>nonsmall cell lung cancer</subject><subject>PASEF</subject><subject>Peptides</subject><subject>Proteins</subject><subject>Proteomes</subject><subject>Proteomics</subject><subject>Scientific imaging</subject><subject>Sensitivity enhancement</subject><issn>1862-8346</issn><issn>1862-8354</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><recordid>eNqFkcluFDEQhluIiITAlSOyxCWXmXjrZY7RKCxSJKIonFuV6uoZR14auzvR3HiEPAhPxZPgZsIcuHCxrdLnr8r-i-Kd4EvBuTwfIsJScqk456V6UZyIppKLRpX65eGsq-PidUr3mdCy5q-KY9XIVSmkOil-XkMEa8kyQJzcZGE0wf_68ZQoGrCsj7Bx5Mc_ZeZo3IaO9SEyM0MdDeOWDTGMFJxBBh7sLpnEQs_uYvC4DWAfKFiIzMIDbIj1djIdw5B74kjZFYNjQ9bnJok9muzzwSeXh2JIebGT3zAEjxTfFEc92ERvn_fT4tvHy9v158XV109f1hdXC1RS1YuqlwC6UkS9oL6sOkClu4aXTaWEQiEIakIStVKAoORKS6wRpWiaRldYq9PibO_NL_s-URpbZ9I8DHgKU2rlSgohSrlSGf3wD3ofppi_YaZKXZU5GpGp5Z7CGFKK1LdDNA7irhW8nXNs5xzbQ475wvtn7XTnqDvgf4PLgN4Dj8bS7j-69vpmfSFlU6vfkkOvOA</recordid><startdate>202403</startdate><enddate>202403</enddate><creator>Vu, Hung M.</creator><creator>Huh, Sunghyun</creator><creator>Lee, Jun Hyung</creator><creator>Lee, Seung Hyeun</creator><creator>Kim, Min‐Sik</creator><general>Wiley Subscription Services, Inc</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-7317-5360</orcidid></search><sort><creationdate>202403</creationdate><title>Parallel accumulation‐serial fragmentation method for in‐depth proteomic analysis of bronchoalveolar lavage fluid collected from patients with nonsmall cell lung cancer</title><author>Vu, Hung M. ; Huh, Sunghyun ; Lee, Jun Hyung ; Lee, Seung Hyeun ; Kim, Min‐Sik</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3237-6f2aa463eef1ef56dac34d80586313c11ea7ece1733aca32942c7cc2188846c73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Accumulation</topic><topic>Alveoli</topic><topic>Biomarkers</topic><topic>bronchoalveolar lavage fluid</topic><topic>Bronchus</topic><topic>Design of experiments</topic><topic>Fragmentation</topic><topic>Ionic mobility</topic><topic>Lavage</topic><topic>Lung cancer</topic><topic>Mass spectrometers</topic><topic>Mass spectrometry</topic><topic>Mass spectroscopy</topic><topic>Non-small cell lung carcinoma</topic><topic>nonsmall cell lung cancer</topic><topic>PASEF</topic><topic>Peptides</topic><topic>Proteins</topic><topic>Proteomes</topic><topic>Proteomics</topic><topic>Scientific imaging</topic><topic>Sensitivity enhancement</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Vu, Hung M.</creatorcontrib><creatorcontrib>Huh, Sunghyun</creatorcontrib><creatorcontrib>Lee, Jun Hyung</creatorcontrib><creatorcontrib>Lee, Seung Hyeun</creatorcontrib><creatorcontrib>Kim, Min‐Sik</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Immunology Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Proteomics. Clinical applications</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Vu, Hung M.</au><au>Huh, Sunghyun</au><au>Lee, Jun Hyung</au><au>Lee, Seung Hyeun</au><au>Kim, Min‐Sik</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Parallel accumulation‐serial fragmentation method for in‐depth proteomic analysis of bronchoalveolar lavage fluid collected from patients with nonsmall cell lung cancer</atitle><jtitle>Proteomics. Clinical applications</jtitle><addtitle>Proteomics Clin Appl</addtitle><date>2024-03</date><risdate>2024</risdate><volume>18</volume><issue>2</issue><spage>e2300053</spage><epage>n/a</epage><pages>e2300053-n/a</pages><issn>1862-8346</issn><eissn>1862-8354</eissn><abstract>Purpose
Advances in mass spectrometry‐based quantitative proteomic analysis have successfully demonstrated the in‐depth detection of protein biomarkers in bronchoalveolar lavage fluid (BALF) from patients with lung cancers. Recently, ion mobility technology was incorporated into the mass spectrometers escalating the sensitivity and throughput. Utilizing these advantages, herein, we employed the parallel accumulation–serial fragmentation (PASEF) implanted in a timsTOF Pro mass spectrometer to examine the alteration of BALF proteomes in patients with nonsmall cell lung cancers (NSCLCs).
Experimental design
BALF proteins were processed from patients with NSCLC and analyzed in a timsTOF Pro mass spectrometer with the PASEF method using a peptide input of 100 ng. Label‐free mass spectrometry data were analyzed in the FragPipe platform.
Results
We quantitated over 1400 proteins from a single injection of 100 ng of peptides per sample with a median of ∼2000 proteins. We were able to find a few potential biomarker proteins upregulated in NSCLC.
Conclusions and clinical relevance
The alterations of the BALF proteome landscape vary among patients with NSCLC as previously observed in patients with small‐cell lung cancers. The PASEF method has significantly enhanced the sensitivity and throughput, demonstrating its effectiveness in clinical research and application.</abstract><cop>Germany</cop><pub>Wiley Subscription Services, Inc</pub><pmid>38295123</pmid><doi>10.1002/prca.202300053</doi><tpages>5</tpages><orcidid>https://orcid.org/0000-0001-7317-5360</orcidid></addata></record> |
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subjects | Accumulation Alveoli Biomarkers bronchoalveolar lavage fluid Bronchus Design of experiments Fragmentation Ionic mobility Lavage Lung cancer Mass spectrometers Mass spectrometry Mass spectroscopy Non-small cell lung carcinoma nonsmall cell lung cancer PASEF Peptides Proteins Proteomes Proteomics Scientific imaging Sensitivity enhancement |
title | Parallel accumulation‐serial fragmentation method for in‐depth proteomic analysis of bronchoalveolar lavage fluid collected from patients with nonsmall cell lung cancer |
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