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Comparison of targeted peptide quantification assays for reductive dehalogenases by selective reaction monitoring (SRM) and precursor reaction monitoring (PRM)
Targeted absolute protein quantification yields valuable information about physiological adaptation of organisms and is thereby of high interest. Especially for this purpose, two proteomic mass spectrometry-based techniques namely selective reaction monitoring (SRM) and precursor reaction monitoring...
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| Published in: | Analytical and bioanalytical chemistry 2014, Vol.406 (1), p.283-291 |
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| creator | Schiffmann, Christian Hansen, Rasmus Baumann, Sven Kublik, Anja Nielsen, Per Halkjær Adrian, Lorenz von Bergen, Martin Jehmlich, Nico Seifert, Jana |
| description | Targeted absolute protein quantification yields valuable information about physiological adaptation of organisms and is thereby of high interest. Especially for this purpose, two proteomic mass spectrometry-based techniques namely selective reaction monitoring (SRM) and precursor reaction monitoring (PRM) are commonly applied. The objective of this study was to establish an optimal quantification assay for proteins with the focus on those involved in housekeeping functions and putative reductive dehalogenase proteins from the strictly anaerobic bacterium
Dehalococcoides mccartyi
strain CBDB1. This microbe is small and slow-growing; hence, it provides little biomass for comprehensive proteomic analysis. We therefore compared SRM and PRM techniques. Eleven peptides were successfully quantified by both methods. In addition, six peptides were solely quantified by SRM and four by PRM, respectively. Peptides were spiked into a background of
Escherichia coli
lysate and the majority of peptides were quantifiable down to 500 amol absolute on column by both methods. Peptide quantification in CBDB1 lysate resulted in the detection of 15 peptides using SRM and 14 peptides with the PRM assay. Resulting quantification of five dehalogenases revealed copy numbers of |
| doi_str_mv | 10.1007/s00216-013-7451-7 |
| format | article |
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Dehalococcoides mccartyi
strain CBDB1. This microbe is small and slow-growing; hence, it provides little biomass for comprehensive proteomic analysis. We therefore compared SRM and PRM techniques. Eleven peptides were successfully quantified by both methods. In addition, six peptides were solely quantified by SRM and four by PRM, respectively. Peptides were spiked into a background of
Escherichia coli
lysate and the majority of peptides were quantifiable down to 500 amol absolute on column by both methods. Peptide quantification in CBDB1 lysate resulted in the detection of 15 peptides using SRM and 14 peptides with the PRM assay. Resulting quantification of five dehalogenases revealed copy numbers of <10 to 115 protein molecules per cell indicating clear differences in abundance of RdhA proteins during growth on hexachlorobenzene. Our results indicated that both methods show comparable sensitivity and that the combination of the mass spectrometry assays resulted in higher peptide coverage and thus more reliable protein quantification.
Figure
Dehalococcoides mccartyi strain CBDB1 cultivated on hexachlorobenzene were used to compare two targeted peptide quantification assays for reductive dehalogenases, namely selective reaction monitoring (SRM) and precursor reaction monitoring (PRM)</description><identifier>ISSN: 1618-2642</identifier><identifier>EISSN: 1618-2650</identifier><identifier>DOI: 10.1007/s00216-013-7451-7</identifier><identifier>PMID: 24220761</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Accuracy ; Anaerobiosis ; Analytical Chemistry ; Assaying ; Bacterial Proteins - chemistry ; Bacterial Proteins - metabolism ; Biochemistry ; Biomass ; Characterization and Evaluation of Materials ; Chemistry ; Chemistry and Materials Science ; Chloroflexi - chemistry ; Chloroflexi - drug effects ; Chloroflexi - metabolism ; Chromatography, High Pressure Liquid - methods ; Escherichia coli - chemistry ; Food Science ; Genomes ; Hexachlorobenzene - metabolism ; Hexachlorobenzene - pharmacology ; Hydrolases - chemistry ; Hydrolases - metabolism ; Isoenzymes - chemistry ; Isoenzymes - metabolism ; Laboratory Medicine ; Mass spectrometry ; Metabolism ; Microorganisms ; Monitoring ; Monitoring/Environmental Analysis ; Oxidation-Reduction ; Peptide Fragments - analysis ; Peptides ; Precursors ; Proteins ; Proteomics ; Proteomics - methods ; Reproduction ; Research Paper ; Respiration ; Scientific imaging ; Tandem Mass Spectrometry - methods</subject><ispartof>Analytical and bioanalytical chemistry, 2014, Vol.406 (1), p.283-291</ispartof><rights>Springer-Verlag Berlin Heidelberg 2013</rights><rights>Springer-Verlag Berlin Heidelberg 2014</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c541t-f7d52703ba66f869b7c93ebce472cb61cd02bce5cb3ed665762fb01603af8b0d3</citedby><cites>FETCH-LOGICAL-c541t-f7d52703ba66f869b7c93ebce472cb61cd02bce5cb3ed665762fb01603af8b0d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,786,790,27957,27958</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24220761$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Schiffmann, Christian</creatorcontrib><creatorcontrib>Hansen, Rasmus</creatorcontrib><creatorcontrib>Baumann, Sven</creatorcontrib><creatorcontrib>Kublik, Anja</creatorcontrib><creatorcontrib>Nielsen, Per Halkjær</creatorcontrib><creatorcontrib>Adrian, Lorenz</creatorcontrib><creatorcontrib>von Bergen, Martin</creatorcontrib><creatorcontrib>Jehmlich, Nico</creatorcontrib><creatorcontrib>Seifert, Jana</creatorcontrib><title>Comparison of targeted peptide quantification assays for reductive dehalogenases by selective reaction monitoring (SRM) and precursor reaction monitoring (PRM)</title><title>Analytical and bioanalytical chemistry</title><addtitle>Anal Bioanal Chem</addtitle><addtitle>Anal Bioanal Chem</addtitle><description>Targeted absolute protein quantification yields valuable information about physiological adaptation of organisms and is thereby of high interest. Especially for this purpose, two proteomic mass spectrometry-based techniques namely selective reaction monitoring (SRM) and precursor reaction monitoring (PRM) are commonly applied. The objective of this study was to establish an optimal quantification assay for proteins with the focus on those involved in housekeeping functions and putative reductive dehalogenase proteins from the strictly anaerobic bacterium
Dehalococcoides mccartyi
strain CBDB1. This microbe is small and slow-growing; hence, it provides little biomass for comprehensive proteomic analysis. We therefore compared SRM and PRM techniques. Eleven peptides were successfully quantified by both methods. In addition, six peptides were solely quantified by SRM and four by PRM, respectively. Peptides were spiked into a background of
Escherichia coli
lysate and the majority of peptides were quantifiable down to 500 amol absolute on column by both methods. Peptide quantification in CBDB1 lysate resulted in the detection of 15 peptides using SRM and 14 peptides with the PRM assay. Resulting quantification of five dehalogenases revealed copy numbers of <10 to 115 protein molecules per cell indicating clear differences in abundance of RdhA proteins during growth on hexachlorobenzene. Our results indicated that both methods show comparable sensitivity and that the combination of the mass spectrometry assays resulted in higher peptide coverage and thus more reliable protein quantification.
Figure
Dehalococcoides mccartyi strain CBDB1 cultivated on hexachlorobenzene were used to compare two targeted peptide quantification assays for reductive dehalogenases, namely selective reaction monitoring (SRM) and precursor reaction monitoring (PRM)</description><subject>Accuracy</subject><subject>Anaerobiosis</subject><subject>Analytical Chemistry</subject><subject>Assaying</subject><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - metabolism</subject><subject>Biochemistry</subject><subject>Biomass</subject><subject>Characterization and Evaluation of Materials</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Chloroflexi - chemistry</subject><subject>Chloroflexi - drug effects</subject><subject>Chloroflexi - metabolism</subject><subject>Chromatography, High Pressure Liquid - methods</subject><subject>Escherichia coli - chemistry</subject><subject>Food Science</subject><subject>Genomes</subject><subject>Hexachlorobenzene - metabolism</subject><subject>Hexachlorobenzene - pharmacology</subject><subject>Hydrolases - chemistry</subject><subject>Hydrolases - metabolism</subject><subject>Isoenzymes - chemistry</subject><subject>Isoenzymes - metabolism</subject><subject>Laboratory Medicine</subject><subject>Mass spectrometry</subject><subject>Metabolism</subject><subject>Microorganisms</subject><subject>Monitoring</subject><subject>Monitoring/Environmental Analysis</subject><subject>Oxidation-Reduction</subject><subject>Peptide Fragments - analysis</subject><subject>Peptides</subject><subject>Precursors</subject><subject>Proteins</subject><subject>Proteomics</subject><subject>Proteomics - methods</subject><subject>Reproduction</subject><subject>Research Paper</subject><subject>Respiration</subject><subject>Scientific imaging</subject><subject>Tandem Mass Spectrometry - methods</subject><issn>1618-2642</issn><issn>1618-2650</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><recordid>eNqNks1u1TAQhSMEoqXwAGyQJTZlkTJ27HHuEl1RQGoF4mcdOc7k4iqJUztBuk_TV8VpSoUQiLuyrfnmzJHnZNlzDmccQL-OAIJjDrzItVQ81w-yY468zAUqeHh_l-IoexLjFQBXJcfH2ZGQQoBGfpzdbH0_muCiH5hv2WTCjiZq2Ejj5Bpi17MZJtc6ayaXEBOj2UfW-sACNbOd3A9iDX03nd_RYCJFVu9ZpI7WUiBjbxt7P7jJBzfs2OmXz5evmBnSkEB2DvFW7C_cp8Q9zR61pov07O48yb6dv_26fZ9ffHz3YfvmIrdK8ilvdaOEhqI2iG2Jm1rbTUG1JamFrZHbBkR6KVsX1CAqjaKtgSMUpi1raIqT7HTVHYO_nilOVe-ipa4zA_k5VhwRALUoxGGo1PIQNJmXoKTWB6CAxbJl_D8qN6BLpWSR0Jd_oFd-DkP6yWRTg8ANlJAovlI2-BgDtdUYXG_CvuJQLUmr1qRVKWnV4qFa_L64U57rnpr7jl_RSoBYgTgu66Tw2-h_qv4Exeve_g</recordid><startdate>2014</startdate><enddate>2014</enddate><creator>Schiffmann, Christian</creator><creator>Hansen, Rasmus</creator><creator>Baumann, Sven</creator><creator>Kublik, Anja</creator><creator>Nielsen, Per Halkjær</creator><creator>Adrian, Lorenz</creator><creator>von Bergen, Martin</creator><creator>Jehmlich, Nico</creator><creator>Seifert, Jana</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</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>3V.</scope><scope>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7TA</scope><scope>7TB</scope><scope>7U5</scope><scope>7U7</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8BQ</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>AFKRA</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>F28</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H8D</scope><scope>H8G</scope><scope>HCIFZ</scope><scope>JG9</scope><scope>JQ2</scope><scope>K9.</scope><scope>KB.</scope><scope>KR7</scope><scope>L7M</scope><scope>LK8</scope><scope>L~C</scope><scope>L~D</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PDBOC</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>7QH</scope><scope>7UA</scope></search><sort><creationdate>2014</creationdate><title>Comparison of targeted peptide quantification assays for reductive dehalogenases by selective reaction monitoring (SRM) and precursor reaction monitoring (PRM)</title><author>Schiffmann, Christian ; Hansen, Rasmus ; Baumann, Sven ; Kublik, Anja ; Nielsen, Per Halkjær ; Adrian, Lorenz ; von Bergen, Martin ; Jehmlich, Nico ; Seifert, Jana</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c541t-f7d52703ba66f869b7c93ebce472cb61cd02bce5cb3ed665762fb01603af8b0d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Accuracy</topic><topic>Anaerobiosis</topic><topic>Analytical Chemistry</topic><topic>Assaying</topic><topic>Bacterial Proteins - 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Academic</collection><collection>Aqualine</collection><collection>Water Resources Abstracts</collection><jtitle>Analytical and bioanalytical chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Schiffmann, Christian</au><au>Hansen, Rasmus</au><au>Baumann, Sven</au><au>Kublik, Anja</au><au>Nielsen, Per Halkjær</au><au>Adrian, Lorenz</au><au>von Bergen, Martin</au><au>Jehmlich, Nico</au><au>Seifert, Jana</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparison of targeted peptide quantification assays for reductive dehalogenases by selective reaction monitoring (SRM) and precursor reaction monitoring (PRM)</atitle><jtitle>Analytical and bioanalytical chemistry</jtitle><stitle>Anal Bioanal Chem</stitle><addtitle>Anal Bioanal Chem</addtitle><date>2014</date><risdate>2014</risdate><volume>406</volume><issue>1</issue><spage>283</spage><epage>291</epage><pages>283-291</pages><issn>1618-2642</issn><eissn>1618-2650</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>Targeted absolute protein quantification yields valuable information about physiological adaptation of organisms and is thereby of high interest. Especially for this purpose, two proteomic mass spectrometry-based techniques namely selective reaction monitoring (SRM) and precursor reaction monitoring (PRM) are commonly applied. The objective of this study was to establish an optimal quantification assay for proteins with the focus on those involved in housekeeping functions and putative reductive dehalogenase proteins from the strictly anaerobic bacterium
Dehalococcoides mccartyi
strain CBDB1. This microbe is small and slow-growing; hence, it provides little biomass for comprehensive proteomic analysis. We therefore compared SRM and PRM techniques. Eleven peptides were successfully quantified by both methods. In addition, six peptides were solely quantified by SRM and four by PRM, respectively. Peptides were spiked into a background of
Escherichia coli
lysate and the majority of peptides were quantifiable down to 500 amol absolute on column by both methods. Peptide quantification in CBDB1 lysate resulted in the detection of 15 peptides using SRM and 14 peptides with the PRM assay. Resulting quantification of five dehalogenases revealed copy numbers of <10 to 115 protein molecules per cell indicating clear differences in abundance of RdhA proteins during growth on hexachlorobenzene. Our results indicated that both methods show comparable sensitivity and that the combination of the mass spectrometry assays resulted in higher peptide coverage and thus more reliable protein quantification.
Figure
Dehalococcoides mccartyi strain CBDB1 cultivated on hexachlorobenzene were used to compare two targeted peptide quantification assays for reductive dehalogenases, namely selective reaction monitoring (SRM) and precursor reaction monitoring (PRM)</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>24220761</pmid><doi>10.1007/s00216-013-7451-7</doi><tpages>9</tpages></addata></record> |
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| subjects | Accuracy Anaerobiosis Analytical Chemistry Assaying Bacterial Proteins - chemistry Bacterial Proteins - metabolism Biochemistry Biomass Characterization and Evaluation of Materials Chemistry Chemistry and Materials Science Chloroflexi - chemistry Chloroflexi - drug effects Chloroflexi - metabolism Chromatography, High Pressure Liquid - methods Escherichia coli - chemistry Food Science Genomes Hexachlorobenzene - metabolism Hexachlorobenzene - pharmacology Hydrolases - chemistry Hydrolases - metabolism Isoenzymes - chemistry Isoenzymes - metabolism Laboratory Medicine Mass spectrometry Metabolism Microorganisms Monitoring Monitoring/Environmental Analysis Oxidation-Reduction Peptide Fragments - analysis Peptides Precursors Proteins Proteomics Proteomics - methods Reproduction Research Paper Respiration Scientific imaging Tandem Mass Spectrometry - methods |
| title | Comparison of targeted peptide quantification assays for reductive dehalogenases by selective reaction monitoring (SRM) and precursor reaction monitoring (PRM) |
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