Data-independent-acquisition mass spectrometry for identification of targeted-peptide site-specific modifications
We present a novel strategy based on data-independent acquisition coupled to targeted data extraction for the detection and identification of site-specific modifications of targeted peptides in a completely unbiased manner. This method requires prior knowledge of the site of the modification along t...
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| Veröffentlicht in: | Analytical and bioanalytical chemistry 2015-09, Vol.407 (22), p.6627-6635 |
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| creator | Porter, Caleb J Bereman, Michael S |
| description | We present a novel strategy based on data-independent acquisition coupled to targeted data extraction for the detection and identification of site-specific modifications of targeted peptides in a completely unbiased manner. This method requires prior knowledge of the site of the modification along the peptide backbone from the protein of interest, but not the mass of the modification. The procedure, named multiplex adduct peptide profiling (MAPP), consists of three steps: 1) A fragment-ion tag is extracted from the data, consisting of the b-type and y-type ion series from the N and C-terminus, respectively, up to the amino-acid position that is believed to be modified; 2) MS1 features are matched to the fragment-ion tag in retention-time space, using the isolation window as a pre-filter to enable calculation of the mass of the modification; and 3) modified fragment ions are overlaid with the unmodified fragment ions to verify the mass calculated in step 2. We discuss the development, applications, and limitations of this new method for detection of unknown peptide modifications. We present an application of the method in profiling adducted peptides derived from abundant proteins in biological fluids with the ultimate objective of detecting biomarkers of exposure to reactive species. |
| doi_str_mv | 10.1007/s00216-015-8819-7 |
| format | Article |
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This method requires prior knowledge of the site of the modification along the peptide backbone from the protein of interest, but not the mass of the modification. The procedure, named multiplex adduct peptide profiling (MAPP), consists of three steps: 1) A fragment-ion tag is extracted from the data, consisting of the b-type and y-type ion series from the N and C-terminus, respectively, up to the amino-acid position that is believed to be modified; 2) MS1 features are matched to the fragment-ion tag in retention-time space, using the isolation window as a pre-filter to enable calculation of the mass of the modification; and 3) modified fragment ions are overlaid with the unmodified fragment ions to verify the mass calculated in step 2. We discuss the development, applications, and limitations of this new method for detection of unknown peptide modifications. We present an application of the method in profiling adducted peptides derived from abundant proteins in biological fluids with the ultimate objective of detecting biomarkers of exposure to reactive species.</description><identifier>ISSN: 1618-2642</identifier><identifier>EISSN: 1618-2650</identifier><identifier>DOI: 10.1007/s00216-015-8819-7</identifier><identifier>PMID: 26105512</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>ABC Highlights: authored by Rising Stars and Top Experts ; Algorithms ; Amino acids ; Amino Acids - analysis ; Amino Acids - chemistry ; Analysis ; Analytical Chemistry ; Backbone ; Binding Sites ; Biochemistry ; biomarkers ; Characterization and Evaluation of Materials ; Chemical properties ; Chemistry ; Chemistry and Materials Science ; Chromatography, Liquid - methods ; Data Mining - methods ; Databases, Protein ; Food Science ; Fragmentation ; Identification ; Ions ; Laboratory Medicine ; Mass spectrometry ; Mathematical analysis ; Monitoring/Environmental Analysis ; Multiplexing ; Paper in Forefront ; Peptides ; Peptides - analysis ; Peptides - chemistry ; Profiling ; Protein Binding ; Protein Interaction Mapping - methods ; Proteins ; Proteomics ; Reproducibility of Results ; Scientific imaging ; Sensitivity and Specificity ; Spectrometry, Mass, Electrospray Ionization - methods</subject><ispartof>Analytical and bioanalytical chemistry, 2015-09, Vol.407 (22), p.6627-6635</ispartof><rights>Springer-Verlag Berlin Heidelberg 2015</rights><rights>COPYRIGHT 2015 Springer</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c776t-2ce4d4dd6d67559200a02ef5394a063b1ff82e4285bd1f5d3ac9afea100f1bff3</citedby><cites>FETCH-LOGICAL-c776t-2ce4d4dd6d67559200a02ef5394a063b1ff82e4285bd1f5d3ac9afea100f1bff3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00216-015-8819-7$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00216-015-8819-7$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,780,784,885,27923,27924,41487,42556,51318</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26105512$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Porter, Caleb J</creatorcontrib><creatorcontrib>Bereman, Michael S</creatorcontrib><title>Data-independent-acquisition mass spectrometry for identification of targeted-peptide site-specific modifications</title><title>Analytical and bioanalytical chemistry</title><addtitle>Anal Bioanal Chem</addtitle><addtitle>Anal Bioanal Chem</addtitle><description>We present a novel strategy based on data-independent acquisition coupled to targeted data extraction for the detection and identification of site-specific modifications of targeted peptides in a completely unbiased manner. This method requires prior knowledge of the site of the modification along the peptide backbone from the protein of interest, but not the mass of the modification. The procedure, named multiplex adduct peptide profiling (MAPP), consists of three steps: 1) A fragment-ion tag is extracted from the data, consisting of the b-type and y-type ion series from the N and C-terminus, respectively, up to the amino-acid position that is believed to be modified; 2) MS1 features are matched to the fragment-ion tag in retention-time space, using the isolation window as a pre-filter to enable calculation of the mass of the modification; and 3) modified fragment ions are overlaid with the unmodified fragment ions to verify the mass calculated in step 2. We discuss the development, applications, and limitations of this new method for detection of unknown peptide modifications. We present an application of the method in profiling adducted peptides derived from abundant proteins in biological fluids with the ultimate objective of detecting biomarkers of exposure to reactive species.</description><subject>ABC Highlights: authored by Rising Stars and Top Experts</subject><subject>Algorithms</subject><subject>Amino acids</subject><subject>Amino Acids - analysis</subject><subject>Amino Acids - chemistry</subject><subject>Analysis</subject><subject>Analytical Chemistry</subject><subject>Backbone</subject><subject>Binding Sites</subject><subject>Biochemistry</subject><subject>biomarkers</subject><subject>Characterization and Evaluation of Materials</subject><subject>Chemical properties</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Chromatography, Liquid - methods</subject><subject>Data Mining - methods</subject><subject>Databases, Protein</subject><subject>Food Science</subject><subject>Fragmentation</subject><subject>Identification</subject><subject>Ions</subject><subject>Laboratory Medicine</subject><subject>Mass spectrometry</subject><subject>Mathematical analysis</subject><subject>Monitoring/Environmental Analysis</subject><subject>Multiplexing</subject><subject>Paper in Forefront</subject><subject>Peptides</subject><subject>Peptides - analysis</subject><subject>Peptides - chemistry</subject><subject>Profiling</subject><subject>Protein Binding</subject><subject>Protein Interaction Mapping - methods</subject><subject>Proteins</subject><subject>Proteomics</subject><subject>Reproducibility of Results</subject><subject>Scientific imaging</subject><subject>Sensitivity and Specificity</subject><subject>Spectrometry, Mass, Electrospray Ionization - methods</subject><issn>1618-2642</issn><issn>1618-2650</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkl9r1jAUxosobk4_gDda8MabzJw0SdsbYWzzDwy80F2HvMlJzWibvkk72Lc3tfNleiEjkISc3_NwcniK4jXQU6C0_pAoZSAJBUGaBlpSPymOQUJDmBT06eHO2VHxIqUbmsEG5PPiiEmgQgA7LvYXetbEjxYnzNs4E232i09-9mEsB51SmSY0cwwDzvGudCGWfuW880b_hoIrZx07nNGSCac5l8usR7IKV6wcgj3g6WXxzOk-4av786S4_nT54_wLufr2-ev52RUxdS1nwgxyy62VVtZCtIxSTRk6UbVcU1ntwLmGIWeN2FlwwlbatNqhzoNxsHOuOik-br7TshvQmtxz1L2aoh90vFNBe_V3ZfQ_VRdulWCiZpRng_f3BjHsF0yzGnwy2Pd6xLAkBTWXTQtQ0cegmRXA2SNQKhlteL028O4f9CYsccxDWynRcglVm6nTjep0j8qPLuTfmLwsDt6EEZ3P72ecSdawGtYOYBOYGFKK6A4zAarWXKktVyrHRa25UnXWvHk4zIPiT5AywDYg5dLYYXzQ639c324ip4PSXfRJXX9nFCRdo1rlz_0CD-Tjvw</recordid><startdate>20150901</startdate><enddate>20150901</enddate><creator>Porter, Caleb J</creator><creator>Bereman, Michael S</creator><general>Springer Berlin Heidelberg</general><general>Springer</general><general>Springer Nature B.V</general><scope>FBQ</scope><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>AEUYN</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>7X8</scope><scope>7QH</scope><scope>7UA</scope><scope>5PM</scope></search><sort><creationdate>20150901</creationdate><title>Data-independent-acquisition mass spectrometry for identification of targeted-peptide site-specific modifications</title><author>Porter, Caleb J ; Bereman, Michael S</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c776t-2ce4d4dd6d67559200a02ef5394a063b1ff82e4285bd1f5d3ac9afea100f1bff3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>ABC Highlights: authored by Rising Stars and Top Experts</topic><topic>Algorithms</topic><topic>Amino acids</topic><topic>Amino Acids - analysis</topic><topic>Amino Acids - chemistry</topic><topic>Analysis</topic><topic>Analytical Chemistry</topic><topic>Backbone</topic><topic>Binding Sites</topic><topic>Biochemistry</topic><topic>biomarkers</topic><topic>Characterization and Evaluation of Materials</topic><topic>Chemical properties</topic><topic>Chemistry</topic><topic>Chemistry and Materials Science</topic><topic>Chromatography, Liquid - methods</topic><topic>Data Mining - methods</topic><topic>Databases, Protein</topic><topic>Food Science</topic><topic>Fragmentation</topic><topic>Identification</topic><topic>Ions</topic><topic>Laboratory Medicine</topic><topic>Mass spectrometry</topic><topic>Mathematical analysis</topic><topic>Monitoring/Environmental Analysis</topic><topic>Multiplexing</topic><topic>Paper in Forefront</topic><topic>Peptides</topic><topic>Peptides - analysis</topic><topic>Peptides - chemistry</topic><topic>Profiling</topic><topic>Protein Binding</topic><topic>Protein Interaction Mapping - methods</topic><topic>Proteins</topic><topic>Proteomics</topic><topic>Reproducibility of Results</topic><topic>Scientific imaging</topic><topic>Sensitivity and Specificity</topic><topic>Spectrometry, Mass, Electrospray Ionization - methods</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Porter, Caleb J</creatorcontrib><creatorcontrib>Bereman, Michael S</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics & Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>ANTE: Abstracts in New Technology & Engineering</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Aerospace Database</collection><collection>Copper Technical Reference Library</collection><collection>SciTech Premium Collection</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>ProQuest Biological Science Collection</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Materials Science Collection</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>MEDLINE - Academic</collection><collection>Aqualine</collection><collection>Water Resources Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Analytical and bioanalytical chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Porter, Caleb J</au><au>Bereman, Michael S</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Data-independent-acquisition mass spectrometry for identification of targeted-peptide site-specific modifications</atitle><jtitle>Analytical and bioanalytical chemistry</jtitle><stitle>Anal Bioanal Chem</stitle><addtitle>Anal Bioanal Chem</addtitle><date>2015-09-01</date><risdate>2015</risdate><volume>407</volume><issue>22</issue><spage>6627</spage><epage>6635</epage><pages>6627-6635</pages><issn>1618-2642</issn><eissn>1618-2650</eissn><abstract>We present a novel strategy based on data-independent acquisition coupled to targeted data extraction for the detection and identification of site-specific modifications of targeted peptides in a completely unbiased manner. This method requires prior knowledge of the site of the modification along the peptide backbone from the protein of interest, but not the mass of the modification. The procedure, named multiplex adduct peptide profiling (MAPP), consists of three steps: 1) A fragment-ion tag is extracted from the data, consisting of the b-type and y-type ion series from the N and C-terminus, respectively, up to the amino-acid position that is believed to be modified; 2) MS1 features are matched to the fragment-ion tag in retention-time space, using the isolation window as a pre-filter to enable calculation of the mass of the modification; and 3) modified fragment ions are overlaid with the unmodified fragment ions to verify the mass calculated in step 2. We discuss the development, applications, and limitations of this new method for detection of unknown peptide modifications. We present an application of the method in profiling adducted peptides derived from abundant proteins in biological fluids with the ultimate objective of detecting biomarkers of exposure to reactive species.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>26105512</pmid><doi>10.1007/s00216-015-8819-7</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | ABC Highlights: authored by Rising Stars and Top Experts Algorithms Amino acids Amino Acids - analysis Amino Acids - chemistry Analysis Analytical Chemistry Backbone Binding Sites Biochemistry biomarkers Characterization and Evaluation of Materials Chemical properties Chemistry Chemistry and Materials Science Chromatography, Liquid - methods Data Mining - methods Databases, Protein Food Science Fragmentation Identification Ions Laboratory Medicine Mass spectrometry Mathematical analysis Monitoring/Environmental Analysis Multiplexing Paper in Forefront Peptides Peptides - analysis Peptides - chemistry Profiling Protein Binding Protein Interaction Mapping - methods Proteins Proteomics Reproducibility of Results Scientific imaging Sensitivity and Specificity Spectrometry, Mass, Electrospray Ionization - methods |
| title | Data-independent-acquisition mass spectrometry for identification of targeted-peptide site-specific modifications |
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