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The plasma peptides of sepsis
A practical strategy to discover sepsis specific proteins may be to compare the plasma peptides and proteins from patients in the intensive care unit with and without sepsis. The aim was to discover proteins and/or peptides that show greater observation frequency and/or precursor intensity in sepsis...
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| Published in: | Clinical proteomics 2020-07, Vol.17 (1), p.26-26, Article 26 |
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| creator | Thavarajah, Thanusi Dos Santos, Claudia C Slutsky, Arthur S Marshall, John C Bowden, Pete Romaschin, Alexander Marshall, John G |
| description | A practical strategy to discover sepsis specific proteins may be to compare the plasma peptides and proteins from patients in the intensive care unit with and without sepsis. The aim was to discover proteins and/or peptides that show greater observation frequency and/or precursor intensity in sepsis. The endogenous tryptic peptides of ICU-Sepsis were compared to ICU Control, ovarian cancer, breast cancer, female normal, sepsis, heart attack, Alzheimer's and multiple sclerosis along with their institution-matched controls, female normals and normal samples collected directly onto ice.
Endogenous tryptic peptides were extracted from individual sepsis and control EDTA plasma samples in a step gradient of acetonitrile for random and independent sampling by LC-ESI-MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were fit to fully tryptic peptides within proteins using the X!TANDEM algorithm. The protein observation frequency was counted using the SEQUEST algorithm after selecting the single best charge state and peptide sequence for each MS/MS spectra. The protein observation frequency of ICU-sepsis versus ICU Control was subsequently tested by Chi square analysis. The average protein or peptide log
precursor intensity was compared across disease and control treatments by ANOVA in the R statistical system.
Peptides and/or phosphopeptides of common plasma proteins such as ITIH3, SAA2, SAA1, and FN1 showed increased observation frequency by Chi square (χ
> 9, p |
| doi_str_mv | 10.1186/s12014-020-09288-5 |
| format | article |
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Endogenous tryptic peptides were extracted from individual sepsis and control EDTA plasma samples in a step gradient of acetonitrile for random and independent sampling by LC-ESI-MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were fit to fully tryptic peptides within proteins using the X!TANDEM algorithm. The protein observation frequency was counted using the SEQUEST algorithm after selecting the single best charge state and peptide sequence for each MS/MS spectra. The protein observation frequency of ICU-sepsis versus ICU Control was subsequently tested by Chi square analysis. The average protein or peptide log
precursor intensity was compared across disease and control treatments by ANOVA in the R statistical system.
Peptides and/or phosphopeptides of common plasma proteins such as ITIH3, SAA2, SAA1, and FN1 showed increased observation frequency by Chi square (χ
> 9, p < 0.003) and/or precursor intensity in sepsis. Cellular gene symbols with large Chi square values from tryptic peptides included POTEB, CTNNA1, U2SURP, KIF24, NLGN2, KSR1, GTF2H1, KIT, RPS6KL1, VAV2, HSPA7, SMC2, TCEB3B, ZNF300, SUPV3L1, ADAMTS20, LAMB4, MCCC1, SUPT6H, SCN9A, SBNO1, EPHA1, ABLIM2, cB5E3.2, EPHA10, GRIN2B, HIVEP2, CCL16, TKT, LRP2 and TMF1 amongst others showed increased observation frequency. Similarly, increased frequency of tryptic phosphopeptides were observed from POM121C, SCN8A, TMED8, NSUN7, SLX4, MADD, DNLZ, PDE3B, UTY, DEPDC7, MTX1, MYO1E, RXRB, SYDE1, FN1, PUS7L, FYCO1, USP26, ACAP2, AHI1, KSR2, LMAN1, ZNF280D and SLC8A2 amongst others. Increases in mean precursor intensity in peptides from common plasma proteins such as ITIH3, SAA2, SAA1, and FN1 as well as cellular proteins such as COL24A1, POTEB, KANK1, SDCBP2, DNAH11, ADAMTS7, MLLT1, TTC21A, TSHR, SLX4, MTCH1, and PUS7L among others were associated with sepsis. The processing of SAA1 included the cleavage of the terminal peptide D/PNHFRPAGLPEKY from the most hydrophilic point of SAA1 on the COOH side of the cystatin C binding that was most apparent in ICU-Sepsis patients compared to all other diseases and controls. Additional cleavage of SAA1 on the NH2 terminus side of the cystatin binding site were observed in ICU-Sepsis. Thus there was disease associated variation in the processing of SAA1 in ICU-Sepsis versus ICU controls or other diseases and controls.
Specific proteins and peptides that vary between diseases might be discovered by the random and independent sampling of multiple disease and control plasma from different hospital and clinics by LC-ESI-MS/MS for storage in a relational SQL Server database and analysis with the R statistical system that will be a powerful tool for clinical research. The processing of SAA1 may play an unappreciated role in the inflammatory response to Sepsis.</description><identifier>ISSN: 1542-6416</identifier><identifier>EISSN: 1559-0275</identifier><identifier>DOI: 10.1186/s12014-020-09288-5</identifier><identifier>PMID: 32636717</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Algorithms ; Alzheimer's disease ; Cellular proteins ; Comparative analysis ; EDTA ; Fibronectins ; Heart attack ; Infection ; Multiple sclerosis ; Nitriles ; Ovarian cancer ; Peptides</subject><ispartof>Clinical proteomics, 2020-07, Vol.17 (1), p.26-26, Article 26</ispartof><rights>The Author(s) 2020.</rights><rights>COPYRIGHT 2020 BioMed Central Ltd.</rights><rights>The Author(s) 2020</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c500t-4e94376e5609745d01a4e2fa2670163a4091e6b0bb913554370f054a5c33c5593</citedby><cites>FETCH-LOGICAL-c500t-4e94376e5609745d01a4e2fa2670163a4091e6b0bb913554370f054a5c33c5593</cites><orcidid>0000-0002-7124-1448</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7331219/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7331219/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32636717$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Thavarajah, Thanusi</creatorcontrib><creatorcontrib>Dos Santos, Claudia C</creatorcontrib><creatorcontrib>Slutsky, Arthur S</creatorcontrib><creatorcontrib>Marshall, John C</creatorcontrib><creatorcontrib>Bowden, Pete</creatorcontrib><creatorcontrib>Romaschin, Alexander</creatorcontrib><creatorcontrib>Marshall, John G</creatorcontrib><title>The plasma peptides of sepsis</title><title>Clinical proteomics</title><addtitle>Clin Proteomics</addtitle><description>A practical strategy to discover sepsis specific proteins may be to compare the plasma peptides and proteins from patients in the intensive care unit with and without sepsis. The aim was to discover proteins and/or peptides that show greater observation frequency and/or precursor intensity in sepsis. The endogenous tryptic peptides of ICU-Sepsis were compared to ICU Control, ovarian cancer, breast cancer, female normal, sepsis, heart attack, Alzheimer's and multiple sclerosis along with their institution-matched controls, female normals and normal samples collected directly onto ice.
Endogenous tryptic peptides were extracted from individual sepsis and control EDTA plasma samples in a step gradient of acetonitrile for random and independent sampling by LC-ESI-MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were fit to fully tryptic peptides within proteins using the X!TANDEM algorithm. The protein observation frequency was counted using the SEQUEST algorithm after selecting the single best charge state and peptide sequence for each MS/MS spectra. The protein observation frequency of ICU-sepsis versus ICU Control was subsequently tested by Chi square analysis. The average protein or peptide log
precursor intensity was compared across disease and control treatments by ANOVA in the R statistical system.
Peptides and/or phosphopeptides of common plasma proteins such as ITIH3, SAA2, SAA1, and FN1 showed increased observation frequency by Chi square (χ
> 9, p < 0.003) and/or precursor intensity in sepsis. Cellular gene symbols with large Chi square values from tryptic peptides included POTEB, CTNNA1, U2SURP, KIF24, NLGN2, KSR1, GTF2H1, KIT, RPS6KL1, VAV2, HSPA7, SMC2, TCEB3B, ZNF300, SUPV3L1, ADAMTS20, LAMB4, MCCC1, SUPT6H, SCN9A, SBNO1, EPHA1, ABLIM2, cB5E3.2, EPHA10, GRIN2B, HIVEP2, CCL16, TKT, LRP2 and TMF1 amongst others showed increased observation frequency. Similarly, increased frequency of tryptic phosphopeptides were observed from POM121C, SCN8A, TMED8, NSUN7, SLX4, MADD, DNLZ, PDE3B, UTY, DEPDC7, MTX1, MYO1E, RXRB, SYDE1, FN1, PUS7L, FYCO1, USP26, ACAP2, AHI1, KSR2, LMAN1, ZNF280D and SLC8A2 amongst others. Increases in mean precursor intensity in peptides from common plasma proteins such as ITIH3, SAA2, SAA1, and FN1 as well as cellular proteins such as COL24A1, POTEB, KANK1, SDCBP2, DNAH11, ADAMTS7, MLLT1, TTC21A, TSHR, SLX4, MTCH1, and PUS7L among others were associated with sepsis. The processing of SAA1 included the cleavage of the terminal peptide D/PNHFRPAGLPEKY from the most hydrophilic point of SAA1 on the COOH side of the cystatin C binding that was most apparent in ICU-Sepsis patients compared to all other diseases and controls. Additional cleavage of SAA1 on the NH2 terminus side of the cystatin binding site were observed in ICU-Sepsis. Thus there was disease associated variation in the processing of SAA1 in ICU-Sepsis versus ICU controls or other diseases and controls.
Specific proteins and peptides that vary between diseases might be discovered by the random and independent sampling of multiple disease and control plasma from different hospital and clinics by LC-ESI-MS/MS for storage in a relational SQL Server database and analysis with the R statistical system that will be a powerful tool for clinical research. The processing of SAA1 may play an unappreciated role in the inflammatory response to Sepsis.</description><subject>Algorithms</subject><subject>Alzheimer's disease</subject><subject>Cellular proteins</subject><subject>Comparative analysis</subject><subject>EDTA</subject><subject>Fibronectins</subject><subject>Heart attack</subject><subject>Infection</subject><subject>Multiple sclerosis</subject><subject>Nitriles</subject><subject>Ovarian cancer</subject><subject>Peptides</subject><issn>1542-6416</issn><issn>1559-0275</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><recordid>eNptkVtLAzEQhYMo3v-AoBQE8WXrTG67-yKIeIOCL_U5pNvZNrK7WTdbwX9vamuxIHlImHznMDOHsTOEIWKmbwJyQJkAhwRynmWJ2mGHqFQeS6naXb4lT7REfcCOQngH4LnMs312ILgWOsX0kJ2P5zRoKxtqO2ip7d2UwsCXg0BtcOGE7ZW2CnS6vo_Z2-PD-P45Gb0-vdzfjZJCAfSJpFyKVJPSkKdSTQGtJF5arlNALayEHElPYDLJUSgVWShBSasKIYrYrzhmtyvfdjGpaVpQ03e2Mm3natt9GW-d2f5p3NzM_KdJhUCOS4PrtUHnPxYUelO7UFBV2Yb8IhguOUqNADqilyt0Zisyril9dCyWuLnTPNORRIzU8B8qninVrvANlS7WtwRXfwRzslU_D75a9M43YRvkK7DofAgdlZsxEcwyV7PK1cRczU-uRkXRxd8FbSS_QYpvfTyZBQ</recordid><startdate>20200702</startdate><enddate>20200702</enddate><creator>Thavarajah, Thanusi</creator><creator>Dos Santos, Claudia C</creator><creator>Slutsky, Arthur S</creator><creator>Marshall, John C</creator><creator>Bowden, Pete</creator><creator>Romaschin, Alexander</creator><creator>Marshall, John G</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-7124-1448</orcidid></search><sort><creationdate>20200702</creationdate><title>The plasma peptides of sepsis</title><author>Thavarajah, Thanusi ; Dos Santos, Claudia C ; Slutsky, Arthur S ; Marshall, John C ; Bowden, Pete ; Romaschin, Alexander ; Marshall, John G</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c500t-4e94376e5609745d01a4e2fa2670163a4091e6b0bb913554370f054a5c33c5593</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Algorithms</topic><topic>Alzheimer's disease</topic><topic>Cellular proteins</topic><topic>Comparative analysis</topic><topic>EDTA</topic><topic>Fibronectins</topic><topic>Heart attack</topic><topic>Infection</topic><topic>Multiple sclerosis</topic><topic>Nitriles</topic><topic>Ovarian cancer</topic><topic>Peptides</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Thavarajah, Thanusi</creatorcontrib><creatorcontrib>Dos Santos, Claudia C</creatorcontrib><creatorcontrib>Slutsky, Arthur S</creatorcontrib><creatorcontrib>Marshall, John C</creatorcontrib><creatorcontrib>Bowden, Pete</creatorcontrib><creatorcontrib>Romaschin, Alexander</creatorcontrib><creatorcontrib>Marshall, John G</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Clinical proteomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Thavarajah, Thanusi</au><au>Dos Santos, Claudia C</au><au>Slutsky, Arthur S</au><au>Marshall, John C</au><au>Bowden, Pete</au><au>Romaschin, Alexander</au><au>Marshall, John G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The plasma peptides of sepsis</atitle><jtitle>Clinical proteomics</jtitle><addtitle>Clin Proteomics</addtitle><date>2020-07-02</date><risdate>2020</risdate><volume>17</volume><issue>1</issue><spage>26</spage><epage>26</epage><pages>26-26</pages><artnum>26</artnum><issn>1542-6416</issn><eissn>1559-0275</eissn><abstract>A practical strategy to discover sepsis specific proteins may be to compare the plasma peptides and proteins from patients in the intensive care unit with and without sepsis. The aim was to discover proteins and/or peptides that show greater observation frequency and/or precursor intensity in sepsis. The endogenous tryptic peptides of ICU-Sepsis were compared to ICU Control, ovarian cancer, breast cancer, female normal, sepsis, heart attack, Alzheimer's and multiple sclerosis along with their institution-matched controls, female normals and normal samples collected directly onto ice.
Endogenous tryptic peptides were extracted from individual sepsis and control EDTA plasma samples in a step gradient of acetonitrile for random and independent sampling by LC-ESI-MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were fit to fully tryptic peptides within proteins using the X!TANDEM algorithm. The protein observation frequency was counted using the SEQUEST algorithm after selecting the single best charge state and peptide sequence for each MS/MS spectra. The protein observation frequency of ICU-sepsis versus ICU Control was subsequently tested by Chi square analysis. The average protein or peptide log
precursor intensity was compared across disease and control treatments by ANOVA in the R statistical system.
Peptides and/or phosphopeptides of common plasma proteins such as ITIH3, SAA2, SAA1, and FN1 showed increased observation frequency by Chi square (χ
> 9, p < 0.003) and/or precursor intensity in sepsis. Cellular gene symbols with large Chi square values from tryptic peptides included POTEB, CTNNA1, U2SURP, KIF24, NLGN2, KSR1, GTF2H1, KIT, RPS6KL1, VAV2, HSPA7, SMC2, TCEB3B, ZNF300, SUPV3L1, ADAMTS20, LAMB4, MCCC1, SUPT6H, SCN9A, SBNO1, EPHA1, ABLIM2, cB5E3.2, EPHA10, GRIN2B, HIVEP2, CCL16, TKT, LRP2 and TMF1 amongst others showed increased observation frequency. Similarly, increased frequency of tryptic phosphopeptides were observed from POM121C, SCN8A, TMED8, NSUN7, SLX4, MADD, DNLZ, PDE3B, UTY, DEPDC7, MTX1, MYO1E, RXRB, SYDE1, FN1, PUS7L, FYCO1, USP26, ACAP2, AHI1, KSR2, LMAN1, ZNF280D and SLC8A2 amongst others. Increases in mean precursor intensity in peptides from common plasma proteins such as ITIH3, SAA2, SAA1, and FN1 as well as cellular proteins such as COL24A1, POTEB, KANK1, SDCBP2, DNAH11, ADAMTS7, MLLT1, TTC21A, TSHR, SLX4, MTCH1, and PUS7L among others were associated with sepsis. The processing of SAA1 included the cleavage of the terminal peptide D/PNHFRPAGLPEKY from the most hydrophilic point of SAA1 on the COOH side of the cystatin C binding that was most apparent in ICU-Sepsis patients compared to all other diseases and controls. Additional cleavage of SAA1 on the NH2 terminus side of the cystatin binding site were observed in ICU-Sepsis. Thus there was disease associated variation in the processing of SAA1 in ICU-Sepsis versus ICU controls or other diseases and controls.
Specific proteins and peptides that vary between diseases might be discovered by the random and independent sampling of multiple disease and control plasma from different hospital and clinics by LC-ESI-MS/MS for storage in a relational SQL Server database and analysis with the R statistical system that will be a powerful tool for clinical research. The processing of SAA1 may play an unappreciated role in the inflammatory response to Sepsis.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>32636717</pmid><doi>10.1186/s12014-020-09288-5</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0002-7124-1448</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Clinical proteomics, 2020-07, Vol.17 (1), p.26-26, Article 26 |
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| language | eng |
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| source | PubMed Central |
| subjects | Algorithms Alzheimer's disease Cellular proteins Comparative analysis EDTA Fibronectins Heart attack Infection Multiple sclerosis Nitriles Ovarian cancer Peptides |
| title | The plasma peptides of sepsis |
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