{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T18:31:28Z","timestamp":1787164288659,"version":"build-2736575974"},"update-to":[{"DOI":"10.12688\/f1000research.13964.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,10,9]],"date-time":"2018-10-09T00:00:00Z","timestamp":1539043200000}}],"reference-count":96,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2018,10,9]],"date-time":"2018-10-09T00:00:00Z","timestamp":1539043200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003130","name":"Fonds Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["757003"],"award-info":[{"award-number":["757003"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns4:p>\n                    <ns4:bold>Background:<\/ns4:bold>\n                    Current syphilis diagnostic strategies are lacking a sensitive manner of directly detecting\n                    <ns4:italic>Treponema pallidum<\/ns4:italic>\n                    antigens. A diagnostic test that could directly detect\n                    <ns4:italic>T. pallidum<\/ns4:italic>\n                    antigens in individuals with syphilis would be of considerable clinical utility, especially for the diagnosis of reinfections and for post-treatment serological follow-up.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Methods:<\/ns4:bold>\n                    In this study, 11 candidate\n                    <ns4:italic>T. pallidum<\/ns4:italic>\n                    biomarker proteins were chosen according to their physiochemical characteristics,\n                    <ns4:italic>T. pallidum<\/ns4:italic>\n                    specificity and predicted abundance. Thirty isotopically labelled proteotypic surrogate peptides (hPTPs) were synthesized and incorporated into a scheduled multiple reaction monitoring assay. Protein extracts from undepleted\/unenriched plasma (N = 18) and urine (N = 4) samples from 18 individuals with syphilis in various clinical stages were tryptically digested, spiked with the hPTP mixture and analysed with a triple quadruple mass spectrometer.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Results:<\/ns4:bold>\n                    No endogenous PTPs corresponding to the eleven candidate biomarkers were detected in any samples analysed. To estimate the Limit of Detection (LOD) of a comparably sensitive mass spectrometer (LTQ-Orbitrap), two dilution series of rabbit cultured purified\n                    <ns4:italic>T. pallidum<\/ns4:italic>\n                    were prepared in PBS. Polyclonal anti-\n                    <ns4:italic>T. pallidum<\/ns4:italic>\n                    antibodies coupled to magnetic Dynabeads were used to enrich one sample series; no LOD improvement was found compared to the unenriched series. The estimated LOD of MS instruments is 300\n                    <ns4:italic>T. pallidum<\/ns4:italic>\n                    \/ml in PBS.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Conclusions:<\/ns4:bold>\n                    Biomarker protein detection likely failed due to the low (femtomoles\/liter) predicted concentration of\n                    <ns4:italic>T. pallidum<\/ns4:italic>\n                    proteins. Alternative sample preparation strategies may improve the detectability of\n                    <ns4:italic>T. pallidum<\/ns4:italic>\n                    proteins in biofluids.\n                  <\/ns4:p>","DOI":"10.12688\/f1000research.13964.2","type":"journal-article","created":{"date-parts":[[2018,10,9]],"date-time":"2018-10-09T04:00:23Z","timestamp":1539057623000},"page":"336","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["Needle lost in the haystack: multiple reaction monitoring fails to detect Treponema pallidum candidate protein biomarkers in plasma and urine samples from individuals with syphilis"],"prefix":"10.12688","volume":"7","author":[{"given":"Geert A.","family":"Van Raemdonck","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8612-8413","authenticated-orcid":false,"given":"Kara K.","family":"Osbak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xaveer","family":"Van Ostade","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chris R.","family":"Kenyon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2018,10,9]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01153-18","article-title":"Long-Term In Vitro Culture of the Syphilis Spirochete Treponema pallidum subsp. pallidum.","volume":"9","author":"D Edmondson","year":"2018","journal-title":"mBio."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"e0143304","DOI":"10.1371\/journal.pone.0143304","article-title":"Global Estimates of the Prevalence and Incidence of Four Curable Sexually Transmitted Infections in 2012 Based on Systematic Review and Global Reporting.","volume":"10","author":"L Newman","year":"2015","journal-title":"PLoS One."},{"key":"ref-3","doi-asserted-by":"crossref","DOI":"10.2807\/ese.17.29.20225-en","article-title":"Increasing trends of gonorrhoea and syphilis and the threat of drug-resistant gonorrhoea in Europe.","volume":"17","author":"M Van de Laar","year":"2012","journal-title":"Euro Surveill."},{"key":"ref-4","doi-asserted-by":"publisher","first-page":"161-8","DOI":"10.1586\/14787210.2015.990384","article-title":"Syphilis in the United States: on the rise?","volume":"13","author":"T Peterman","year":"2015","journal-title":"Expert Rev Anti Infect Ther."},{"key":"ref-5","doi-asserted-by":"publisher","first-page":"20958","DOI":"10.2807\/1560-7917.ES2014.19.45.20958","article-title":"Syphilis reinfections pose problems for syphilis diagnosis in Antwerp, Belgium - 1992 to 2012.","volume":"19","author":"C Kenyon","year":"2014","journal-title":"Euro Surveill."},{"key":"ref-6","doi-asserted-by":"publisher","first-page":"1554-8","DOI":"10.1086\/598997","article-title":"A population-based study of infectious syphilis rediagnosis in British Columbia, 1995-2005.","volume":"48","author":"G Ogilvie","year":"2009","journal-title":"Clin Infect Dis."},{"key":"ref-7","doi-asserted-by":"publisher","first-page":"700-8","DOI":"10.1086\/655832","article-title":"Novel Treponema pallidum serologic tests: a paradigm shift in syphilis screening for the 21st century.","volume":"51","author":"A Se\u00f1a","year":"2010","journal-title":"Clin Infect Dis."},{"key":"ref-8","doi-asserted-by":"publisher","first-page":"2151-7","DOI":"10.1128\/jb.176.8.2151-2157.1994","article-title":"Fatty acids of Treponema pallidum and Borrelia burgdorferi lipoproteins.","volume":"176","author":"J Belisle","year":"1994","journal-title":"J Bacteriol."},{"key":"ref-9","doi-asserted-by":"publisher","first-page":"569-71","DOI":"10.1097\/00007435-199811000-00013","article-title":"The association of false-positive rapid plasma reagin results and HIV infection.","volume":"25","author":"P Joyanes","year":"1998","journal-title":"Sex Transm Dis."},{"key":"ref-10","doi-asserted-by":"publisher","first-page":"1645-50","DOI":"10.1016\/j.vaccine.2008.10.084","article-title":"Possible autoimmune reactions following smallpox vaccination: the biologic false positive test for syphilis.","volume":"27","author":"T Monath","year":"2009","journal-title":"Vaccine."},{"key":"ref-11","doi-asserted-by":"publisher","first-page":"1092-9","DOI":"10.1093\/cid\/cir671","article-title":"Predictors of serological cure and Serofast State after treatment in HIV-negative persons with early syphilis.","volume":"53","author":"A Se\u00f1a","year":"2011","journal-title":"Clin Infect Dis."},{"key":"ref-12","doi-asserted-by":"publisher","first-page":"251-6","DOI":"10.1136\/sextrans-2012-050622","article-title":"Sensitivity, specificity and likelihood ratios of PCR in the diagnosis of syphilis: a systematic review and meta-analysis.","volume":"89","author":"A Gayet-Ageron","year":"2013","journal-title":"Sex Transm Infect."},{"key":"ref-13","doi-asserted-by":"publisher","first-page":"479-85","DOI":"10.1136\/sti.2011.049494","article-title":"Getting the measure of syphilis: qPCR to better understand early infection.","volume":"87","author":"C Tipple","year":"2011","journal-title":"Sex Transm Infect."},{"key":"ref-14","doi-asserted-by":"publisher","first-page":"842-5","DOI":"10.1258\/095646207782716901","article-title":"Detection of Treponema pallidum sp pallidum DNA in latent syphilis.","volume":"18","author":"R Castro","year":"2007","journal-title":"Int J STD AIDS."},{"key":"ref-15","doi-asserted-by":"publisher","first-page":"e74319","DOI":"10.1371\/journal.pone.0074319","article-title":"Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: correction of sequencing errors resulted in increased separation of syphilis treponeme subclusters.","volume":"8","author":"H P\u011btro\u0161ov\u00e1","year":"2013","journal-title":"PLoS One."},{"key":"ref-16","doi-asserted-by":"publisher","first-page":"2631-43","DOI":"10.1128\/IAI.00173-10","article-title":"Characterization and serologic analysis of the Treponema pallidum proteome.","volume":"78","author":"M McGill","year":"2010","journal-title":"Infect Immun."},{"key":"ref-17","doi-asserted-by":"publisher","first-page":"e0004988","DOI":"10.1371\/journal.pntd.0004988","article-title":"Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry.","volume":"10","author":"K Osbak","year":"2016","journal-title":"PLoS Negl Trop Dis."},{"key":"ref-18","doi-asserted-by":"publisher","first-page":"1866-74","DOI":"10.1128\/JB.187.5.1866-1874.2005","article-title":"Transcriptome of Treponema pallidum: gene expression profile during experimental rabbit infection.","volume":"187","author":"D Smajs","year":"2005","journal-title":"J Bacteriol."},{"key":"ref-19","doi-asserted-by":"publisher","first-page":"2954-8","DOI":"10.1128\/IAI.00090-07","article-title":"Assessment of the kinetics of Treponema pallidum dissemination into blood and tissues in experimental syphilis by real-time quantitative PCR.","volume":"75","author":"J Salazar","year":"2007","journal-title":"Infect Immun."},{"key":"ref-20","doi-asserted-by":"publisher","first-page":"30-3","DOI":"10.1016\/S0140-6736(98)08103-3","article-title":"Diagnosis of Helicobacter pylori infection with a new non-invasive antigen-based assay. HpSA European study group.","volume":"354","author":"D Vaira","year":"1999","journal-title":"Lancet."},{"key":"ref-21","doi-asserted-by":"publisher","first-page":"1019-23","DOI":"10.1093\/cid\/cir613","article-title":"Evaluation of a novel point-of-care cryptococcal antigen test on serum, plasma, and urine from patients with HIV-associated cryptococcal meningitis.","volume":"53","author":"J Jarvis","year":"2011","journal-title":"Clin Infect Dis."},{"key":"ref-22","doi-asserted-by":"crossref","first-page":"1963-5","DOI":"10.1128\/JCM.33.7.1963-1965.1995","article-title":"Evaluation of new rapid commercial enzyme immunoassay for detection of Cryptosporidium oocysts in untreated stool specimens.","volume":"33","author":"M Parisi","year":"1995","journal-title":"J Clin Microbiol."},{"key":"ref-23","doi-asserted-by":"crossref","first-page":"449-52","DOI":"10.1128\/JCM.36.2.449-452.1998","article-title":"Comparison of PCR, isoenzyme analysis, and antigen detection for diagnosis of Entamoeba histolytica infection.","volume":"36","author":"R Haque","year":"1998","journal-title":"J Clin Microbiol."},{"key":"ref-24","doi-asserted-by":"publisher","first-page":"S210-7","DOI":"10.1093\/infdis\/jiw293","article-title":"Analytical Validation of the ReEBOV Antigen Rapid Test for Point-of-Care Diagnosis of Ebola Virus Infection.","volume":"214","author":"R Cross","year":"2016","journal-title":"J Infect Dis."},{"key":"ref-25","doi-asserted-by":"publisher","first-page":"1616-27","DOI":"10.1128\/CVI.05205-11","article-title":"Systematic review and meta-analysis of antigen detection tests for the diagnosis of tuberculosis.","volume":"18","author":"L Flores","year":"2011","journal-title":"Clin Vaccine Immunol."},{"key":"ref-26","article-title":"Princ. Pract. Infect. Dis.","author":"E Tramont","year":"2015"},{"key":"ref-27","doi-asserted-by":"publisher","first-page":"323-45","DOI":"10.1002\/prca.201500116","article-title":"Clinical applications of MS-based protein quantification.","volume":"10","author":"B Sabbagh","year":"2016","journal-title":"Proteomics Clin Appl."},{"key":"ref-28","doi-asserted-by":"publisher","first-page":"346-57","DOI":"10.1002\/prca.201500086","article-title":"Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria.","volume":"10","author":"K Cheng","year":"2016","journal-title":"Proteomics Clin Appl."},{"key":"ref-29","doi-asserted-by":"publisher","first-page":"6940-5","DOI":"10.1073\/pnas.0832254100","article-title":"Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS.","volume":"100","author":"S Gerber","year":"2003","journal-title":"Proc Natl Acad Sci U S A."},{"key":"ref-30","doi-asserted-by":"publisher","first-page":"175-86","DOI":"10.1038\/nprot.2010.196","article-title":"Absolute quantification of protein and post-translational modification abundance with stable isotope-labeled synthetic peptides.","volume":"6","author":"A Kettenbach","year":"2011","journal-title":"Nat Protoc."},{"key":"ref-31","doi-asserted-by":"publisher","first-page":"1441-54","DOI":"10.1586\/14737159.2015.1093937","article-title":"SRM\/MRM targeted proteomics as a tool for biomarker validation and absolute quantification in human urine.","volume":"15","author":"G Mermelekas","year":"2015","journal-title":"Expert Rev Mol Diagn."},{"key":"ref-32","doi-asserted-by":"publisher","first-page":"431-48","DOI":"10.1586\/14789450.2014.901157","article-title":"Mass spectrometry-based plasma proteomics: state of the art and future outlook.","volume":"11","author":"M Pernemalm","year":"2014","journal-title":"Expert Rev Proteomics."},{"key":"ref-33","doi-asserted-by":"publisher","first-page":"1222-43","DOI":"10.1002\/pmic.201100568","article-title":"MRM-based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma.","volume":"12","author":"D Domanski","year":"2012","journal-title":"Proteomics."},{"key":"ref-34","doi-asserted-by":"publisher","first-page":"2202-15","DOI":"10.1002\/pmic.201200316","article-title":"Multiplexed MRM-based quantitation of candidate cancer biomarker proteins in undepleted and non-enriched human plasma.","volume":"13","author":"A Percy","year":"2013","journal-title":"Proteomics."},{"key":"ref-35","doi-asserted-by":"publisher","first-page":"1860-77","DOI":"10.1074\/mcp.M800540-MCP200","article-title":"Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma.","volume":"8","author":"M Kuzyk","year":"2009","journal-title":"Mol Cell Proteomics."},{"key":"ref-36","doi-asserted-by":"publisher","first-page":"24-33","DOI":"10.1016\/j.ymeth.2015.04.001","article-title":"Precise quantitation of 136 urinary proteins by LC\/MRM-MS using stable isotope labeled peptides as internal standards for biomarker discovery and\/or verification studies.","volume":"81","author":"A Percy","year":"2015","journal-title":"Methods."},{"key":"ref-37","doi-asserted-by":"publisher","first-page":"935-43","DOI":"10.1128\/CVI.00125-12","article-title":"Identification and diagnostic utility of Leishmania infantum proteins found in urine samples from patients with visceral leishmaniasis.","volume":"19","author":"C Abeijon","year":"2012","journal-title":"Clin Vaccine Immunol."},{"key":"ref-38","doi-asserted-by":"publisher","first-page":"e2161","DOI":"10.1371\/journal.pntd.0002161","article-title":"Potential non-invasive urine-based antigen (protein) detection assay to diagnose active visceral leishmaniasis.","volume":"7","author":"C Abeijon","year":"2013","journal-title":"PLoS Negl Trop Dis."},{"key":"ref-39","doi-asserted-by":"publisher","first-page":"e103811","DOI":"10.1371\/journal.pone.0103811","article-title":"Detection of Mycobacterium tuberculosis peptides in the exosomes of patients with active and latent M. tuberculosis infection using MRM-MS.","volume":"9","author":"N Kruh-Garcia","year":"2014","journal-title":"PLoS One."},{"key":"ref-40","doi-asserted-by":"publisher","first-page":"1719-29","DOI":"10.1183\/09031936.00175113","article-title":"The identification of tuberculosis biomarkers in human urine samples.","volume":"43","author":"B Young","year":"2014","journal-title":"Eur Respir J."},{"key":"ref-41","doi-asserted-by":"publisher","first-page":"56-62","DOI":"10.1111\/j.1365-2249.2008.03672.x","article-title":"Identification and characterization of Mycobacterium tuberculosis antigens in urine of patients with active pulmonary tuberculosis: an innovative and alternative approach of antigen discovery of useful microbial molecules.","volume":"153","author":"S Kashino","year":"2008","journal-title":"Clin Exp Immunol."},{"key":"ref-42","doi-asserted-by":"publisher","first-page":"1631-7","DOI":"10.1128\/JCM.00236-16","article-title":"Identification of Mycobacterial Antigens in Human Urine by Use of Immunoglobulin G Isolated from Sera of Patients with Active Pulmonary Tuberculosis.","volume":"54","author":"S Kim","year":"2016","journal-title":"J Clin Microbiol."},{"key":"ref-43","first-page":"1-110","article-title":"Sexually transmitted diseases treatment guidelines, 2010.","volume":"59","author":"K Workowski","year":"2010","journal-title":"MMWR Recomm Rep."},{"key":"ref-44","doi-asserted-by":"publisher","first-page":"300-9","DOI":"10.1258\/ijsa.2008.008510","article-title":"IUSTI: 2008 European Guidelines on the Management of Syphilis.","volume":"20","author":"P French","year":"2009","journal-title":"Int J STD AIDS."},{"key":"ref-45","doi-asserted-by":"publisher","first-page":"1941-6","DOI":"10.1128\/JCM.39.5.1941-1946.2001","article-title":"New tests for syphilis: rational design of a PCR method for detection of Treponema pallidum in clinical specimens using unique regions of the DNA polymerase I gene.","volume":"39","author":"H Liu","year":"2001","journal-title":"J Clin Microbiol."},{"key":"ref-46","doi-asserted-by":"publisher","first-page":"669-74","DOI":"10.2340\/00015555-1335","article-title":"Sequencing-based molecular typing of Treponema pallidum strains in the Czech Republic: all identified genotypes are related to the sequence of the SS14 strain.","volume":"92","author":"M Flasarov\u00e1","year":"2012","journal-title":"Acta Derm Venereol."},{"key":"ref-47","doi-asserted-by":"publisher","first-page":"e0003492","DOI":"10.1371\/journal.pntd.0003492","article-title":"Rapid Treponema pallidum clearance from blood and ulcer samples following single dose benzathine penicillin treatment of early syphilis.","volume":"9","author":"C Tipple","year":"2015","journal-title":"PLoS Negl Trop Dis."},{"key":"ref-48","doi-asserted-by":"publisher","first-page":"3262-77","DOI":"10.1002\/pmic.200401245","article-title":"HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples.","volume":"5","author":"A Rai","year":"2005","journal-title":"Proteomics."},{"key":"ref-49","doi-asserted-by":"publisher","first-page":"e38290","DOI":"10.1371\/journal.pone.0038290","article-title":"The effect of pre-analytical variability on the measurement of MRM-MS-based mid- to high-abundance plasma protein biomarkers and a panel of cytokines.","volume":"7","author":"A Aguilar-Mahecha","year":"2012","journal-title":"PLoS One."},{"key":"ref-50","doi-asserted-by":"publisher","first-page":"239-47","DOI":"10.2144\/05392RR01","article-title":"Artifactual isoform profile modification following treatment of human plasma or serum with protease inhibitor, monitored by 2-dimensional electrophoresis and mass spectrometry.","volume":"39","author":"M Schuchard","year":"2005","journal-title":"Biotechniques."},{"key":"ref-51","article-title":"Human Kidney and Urine Proteome Project."},{"key":"ref-52","doi-asserted-by":"publisher","first-page":"190-8","DOI":"10.1038\/nbt.1524","article-title":"Prediction of high-responding peptides for targeted protein assays by mass spectrometry.","volume":"27","author":"V Fusaro","year":"2009","journal-title":"Nat Biotechnol."},{"key":"ref-53","doi-asserted-by":"publisher","first-page":"403-10","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"S Altschul","year":"1990","journal-title":"J Mol Biol."},{"key":"ref-54","doi-asserted-by":"publisher","first-page":"D655-8","DOI":"10.1093\/nar\/gkj040","article-title":"The PeptideAtlas project.","volume":"34","author":"F Desiere","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref-55","doi-asserted-by":"publisher","DOI":"10.1002\/9780471729259.mc12a01s7","article-title":"Isolation and laboratory maintenance of Treponema pallidum.","volume":"Chapter 12","author":"S Lukehart","year":"2007","journal-title":"Curr Protoc Microbiol."},{"key":"ref-56","doi-asserted-by":"publisher","first-page":"275-86","DOI":"10.1097\/00007435-198410000-00003","article-title":"Purification of Treponema pallidum, Nichols strain, by Percoll density gradient centrifugation.","volume":"11","author":"P Hanff","year":"1984","journal-title":"Sex Transm Dis."},{"key":"ref-57","doi-asserted-by":"publisher","first-page":"375-88","DOI":"10.1126\/science.281.5375.375","article-title":"Complete genome sequence of Treponema pallidum, the syphilis spirochete.","volume":"281","author":"C Fraser","year":"1998","journal-title":"Science."},{"key":"ref-58","doi-asserted-by":"publisher","first-page":"5383-92","DOI":"10.1021\/ac025747h","article-title":"Empirical statistical model to estimate the accuracy of peptide identifications made by MS\/MS and database search.","volume":"74","author":"A Keller","year":"2002","journal-title":"Anal Chem."},{"key":"ref-59","doi-asserted-by":"publisher","first-page":"1496-515","DOI":"10.1111\/j.1365-2958.2011.07662.x","article-title":"TP0326, a Treponema pallidum \u03b2-barrel assembly machinery A (BamA) orthologue and rare outer membrane protein.","volume":"80","author":"D Desrosiers","year":"2011","journal-title":"Mol Microbiol."},{"key":"ref-60","doi-asserted-by":"publisher","first-page":"1401-13","DOI":"10.1086\/315399","article-title":"Opsonic potential, protective capacity, and sequence conservation of the Treponema pallidum subspecies pallidum Tp92.","volume":"181","author":"C Cameron","year":"2000","journal-title":"J Infect Dis."},{"key":"ref-61","doi-asserted-by":"publisher","first-page":"1906-20","DOI":"10.1128\/JB.00086-15","article-title":"A Homology Model Reveals Novel Structural Features and an Immunodominant Surface Loop\/Opsonic Target in the Treponema pallidum BamA Ortholog TP_0326.","volume":"197","author":"A Luthra","year":"2015","journal-title":"J Bacteriol."},{"key":"ref-62","doi-asserted-by":"publisher","first-page":"976-80","DOI":"10.1128\/JCM.03444-14","article-title":"Performance of the 47-kilodalton membrane protein versus DNA polymerase I genes for detection of Treponema pallidum by PCR in ulcers.","volume":"53","author":"A Gayet-Ageron","year":"2015","journal-title":"J Clin Microbiol."},{"key":"ref-63","doi-asserted-by":"publisher","first-page":"e2222","DOI":"10.1371\/journal.pntd.0002222","article-title":"Fine analysis of genetic diversity of the tpr gene family among treponemal species, subspecies and strains.","volume":"7","author":"A Centurion-Lara","year":"2013","journal-title":"PLoS Negl Trop Dis."},{"key":"ref-64","doi-asserted-by":"publisher","first-page":"481-7","DOI":"10.7883\/yoken.JJID.2014.416","article-title":"Development of a Multiplex Real-Time PCR Assay for the Detection of Treponema pallidum, HCV, HIV-1, and HBV.","volume":"68","author":"L Zhou","year":"2015","journal-title":"Jpn J Infect Dis."},{"key":"ref-65","doi-asserted-by":"publisher","first-page":"e690","DOI":"10.1371\/journal.pntd.0000690","article-title":"Secondary syphilis in cali, Colombia: new concepts in disease pathogenesis.","volume":"4","author":"A Cruz","year":"2010","journal-title":"PLoS Negl Trop Dis."},{"key":"ref-66","doi-asserted-by":"publisher","first-page":"296-302","DOI":"10.1016\/j.micpath.2017.01.059","article-title":"A retrospective cross-sectional quantitative molecular approach in biological samples from patients with syphilis.","volume":"104","author":"M Pinto","year":"2017","journal-title":"Microb Pathog."},{"key":"ref-67","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1186\/1471-2334-12-103","article-title":"Point-of-care detection of lipoarabinomannan (LAM) in urine for diagnosis of HIV-associated tuberculosis: a state of the art review.","volume":"12","author":"S Lawn","year":"2012","journal-title":"BMC Infect Dis."},{"key":"ref-68","doi-asserted-by":"publisher","first-page":"57-68","DOI":"10.1016\/j.jchromb.2016.01.015","article-title":"Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids.","volume":"1021","author":"C Wu","year":"2016","journal-title":"J Chromatogr B Analyt Technol Biomed Life Sci."},{"key":"ref-69","doi-asserted-by":"publisher","first-page":"113-24","DOI":"10.1016\/j.jprot.2014.04.024","article-title":"Enhanced sensitivity and multiplexing with 2D LC\/MRM-MS and labeled standards for deeper and more comprehensive protein quantitation.","volume":"106","author":"A Percy","year":"2014","journal-title":"J Proteomics."},{"key":"ref-70","doi-asserted-by":"publisher","first-page":"1074-92","DOI":"10.1002\/pmic.201100436","article-title":"Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics.","volume":"12","author":"T Shi","year":"2012","journal-title":"Proteomics."},{"key":"ref-71","doi-asserted-by":"publisher","first-page":"2212-29","DOI":"10.1074\/mcp.M700354-MCP200","article-title":"Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution.","volume":"6","author":"H Keshishian","year":"2007","journal-title":"Mol Cell Proteomics."},{"key":"ref-72","doi-asserted-by":"publisher","first-page":"e24442","DOI":"10.1371\/journal.pone.0024442","article-title":"A systematic analysis of eluted fraction of plasma post immunoaffinity depletion: implications in biomarker discovery.","volume":"6","author":"A Yadav","year":"2011","journal-title":"PLoS One."},{"key":"ref-73","doi-asserted-by":"publisher","first-page":"2525-33","DOI":"10.1128\/IAI.71.5.2525-2533.2003","article-title":"Identification of a Treponema pallidum laminin-binding protein.","volume":"71","author":"C Cameron","year":"2003","journal-title":"Infect Immun."},{"key":"ref-74","doi-asserted-by":"publisher","first-page":"7019-22","DOI":"10.1128\/JB.186.20.7019-7022.2004","article-title":"Treponema pallidum fibronectin-binding proteins.","volume":"186","author":"C Cameron","year":"2004","journal-title":"J Bacteriol."},{"key":"ref-75","doi-asserted-by":"publisher","first-page":"1848-57","DOI":"10.1128\/IAI.01424-07","article-title":"A novel Treponema pallidum antigen, TP0136, is an outer membrane protein that binds human fibronectin.","volume":"76","author":"M Brinkman","year":"2008","journal-title":"Infect Immun."},{"key":"ref-76","doi-asserted-by":"publisher","first-page":"2349-57","DOI":"10.1099\/00221287-131-9-2349","article-title":"The outer membrane of Treponema pallidum: biological significance and biochemical properties.","volume":"131","author":"C Penn","year":"1985","journal-title":"J Gen Microbiol."},{"key":"ref-77","doi-asserted-by":"publisher","first-page":"399-410","DOI":"10.1016\/j.clinbiochem.2012.12.019","article-title":"Rapid development of sensitive, high-throughput, quantitative and highly selective mass spectrometric targeted immunoassays for clinically important proteins in human plasma and serum.","volume":"46","author":"B Krastins","year":"2013","journal-title":"Clin Biochem."},{"key":"ref-78","doi-asserted-by":"publisher","first-page":"1153-8","DOI":"10.1021\/ac00103a003","article-title":"Mass Spectrometric Immunoassay.","volume":"67","author":"R Nelson","year":"1995","journal-title":"Anal Chem."},{"key":"ref-79","doi-asserted-by":"publisher","first-page":"737-48","DOI":"10.1021\/ac302071k","article-title":"Mass-linked immuno-selective assays in targeted proteomics.","volume":"85","author":"A Madian","year":"2013","journal-title":"Anal Chem."},{"key":"ref-80","doi-asserted-by":"publisher","first-page":"888-91","DOI":"10.1128\/JCM.44.3.888-891.2006","article-title":"Reactivity of antibodies from syphilis patients to a protein array representing the Treponema pallidum proteome.","volume":"44","author":"M Brinkman","year":"2006","journal-title":"J Clin Microbiol."},{"key":"ref-81","doi-asserted-by":"publisher","first-page":"1133-40","DOI":"10.1016\/S1286-4579(02)01638-6","article-title":"The immune response to infection with Treponema pallidum, the stealth pathogen.","volume":"4","author":"J Salazar","year":"2002","journal-title":"Microbes Infect."},{"key":"ref-82","doi-asserted-by":"publisher","first-page":"29-49","DOI":"10.1128\/CMR.19.1.29-49.2006","article-title":"Biological basis for syphilis.","volume":"19","author":"R Lafond","year":"2006","journal-title":"Clin Microbiol Rev."},{"key":"ref-83","doi-asserted-by":"publisher","first-page":"235-44","DOI":"10.1021\/pr034086h","article-title":"Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA).","volume":"3","author":"N Anderson","year":"2004","journal-title":"J Proteome Res."},{"key":"ref-84","doi-asserted-by":"publisher","first-page":"184-96","DOI":"10.1074\/mcp.M900254-MCP200","article-title":"An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers.","volume":"9","author":"J Whiteaker","year":"2010","journal-title":"Mol Cell Proteomics."},{"key":"ref-85","doi-asserted-by":"publisher","first-page":"289-301","DOI":"10.1111\/j.1574-695X.2007.00303.x","article-title":"Length of guanosine homopolymeric repeats modulates promoter activity of subfamily II tpr genes of Treponema pallidum ssp. pallidum.","volume":"51","author":"L Giacani","year":"2007","journal-title":"FEMS Immunol Med Microbiol."},{"key":"ref-86","doi-asserted-by":"publisher","first-page":"3822-9","DOI":"10.4049\/jimmunol.0902788","article-title":"Antigenic variation in Treponema pallidum: TprK sequence diversity accumulates in response to immune pressure during experimental syphilis.","volume":"184","author":"L Giacani","year":"2010","journal-title":"J Immunol."},{"key":"ref-87","doi-asserted-by":"publisher","first-page":"2199-204","DOI":"10.1073\/pnas.0611217104","article-title":"Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.","volume":"104","author":"H Molina","year":"2007","journal-title":"Proc Natl Acad Sci U S A."},{"key":"ref-88","doi-asserted-by":"publisher","first-page":"5751-4","DOI":"10.5167\/uzh-1654","article-title":"Flagellins, but not endoflagellar sheath proteins, of Treponema pallidum and of pathogen-related oral spirochetes are glycosylated.","volume":"66","author":"C Wyss","year":"1998","journal-title":"Infect Immun."},{"key":"ref-89","doi-asserted-by":"publisher","first-page":"622-35","DOI":"10.1099\/mic.0.054767-0","article-title":"Methylation and in vivo expression of the surfaceexposed Leptospira interrogans outer-membrane protein OmpL32.","volume":"158","author":"A Eshghi","year":"2012","journal-title":"Microbiology."},{"key":"ref-90","doi-asserted-by":"publisher","first-page":"e3280","DOI":"10.1371\/journal.pntd.0003280","article-title":"Post-translational modification of LipL32 during Leptospira interrogans infection.","volume":"8","author":"T Witchell","year":"2014","journal-title":"PLoS Negl Trop Dis."},{"key":"ref-91","first-page":"248-55","article-title":"Reinfection of chancre-immune rabbits with Treponema pallidum. I. Light and immunofluorescence studies.","volume":"118","author":"S Sell","year":"1985","journal-title":"Am J Pathol."},{"key":"ref-92","doi-asserted-by":"publisher","first-page":"222-33","DOI":"10.1021\/pr300893w","article-title":"Standardized protocols for quality control of MRM-based plasma proteomic workflows.","volume":"12","author":"A Percy","year":"2013","journal-title":"J Proteome Res."},{"key":"ref-93","doi-asserted-by":"publisher","first-page":"e71463","DOI":"10.1371\/journal.pone.0071463","article-title":"Identification of Trypanosome proteins in Plasma from African sleeping sickness patients infected with T. b. rhodesiense.","volume":"8","author":"B Eyford","year":"2013","journal-title":"PLoS One."},{"key":"ref-94","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201600278","article-title":"SWATH-MS as a tool for biomarker discovery: From basic research to clinical applications.","volume":"17","author":"S Anjo","year":"2017","journal-title":"Proteomics."},{"key":"ref-95","doi-asserted-by":"publisher","first-page":"665-76","DOI":"10.1021\/acs.jproteome.6b00727","article-title":"Quantitative Proteomics Based on Optimized Data-Independent Acquisition in Plasma Analysis.","volume":"16","author":"E Nigjeh","year":"2017","journal-title":"J Proteome Res."},{"key":"ref-96","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.O111.016717","article-title":"Targeted data extraction of the MS\/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.","volume":"11","author":"L Gillet","year":"2012","journal-title":"Mol Cell Proteomics."}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/7-336\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/7-336\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/7-336\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,3]],"date-time":"2022-09-03T12:57:38Z","timestamp":1662209858000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/7-336\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,10,9]]},"references-count":96,"URL":"https:\/\/doi.org\/10.12688\/f1000research.13964.2","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.18062.r39229","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.18062.r39229","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,10,9]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/7-336\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.18062.r39229, Mohd M. Khan, University of Maryland, Baltimore, MD, USA, 19 Nov 2018, version 2, indexed","URL":"https:\/\/f1000research.com\/articles\/7-336\/v2#referee-response-39229","order":0,"name":"referee-response-39229","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.15178.r35202, Timothy Palzkill, Department\u00a0of\u00a0Pharmacology\u00a0and\u00a0Chemical Biology, Baylor College of Medicine, Houston, TX, USA, 22 Aug 2018, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/7-336\/v1#referee-response-35202","order":1,"name":"referee-response-35202","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Kara Osbak<\/b>; <i>Posted: 03 Oct 2018<\/i>; 1. <b>Some of the description of LOD experiments with dilutions of T. pallidum on page 7, right column, paragraph 2, is difficult to follow. The authors state \u201cIn total, eight unique T. pallidum proteins were found in the unenriched and enriched retentate\u2026\u201d but they do not state a dilution. Later in the paragraph, it states \u201cTen unique T. pallidum proteins were found in the highest concentration\u2026.\u201d . This is confusing. What condition does the eight unique proteins refer to?<\/b> &nbsp; This ambiguous sentence has now been reworded- \u201cIn total, eight unique <i>T. pallidum<\/i> proteins were found in both the unenriched and enriched retentate dilution series in one or more of the concentrations analyzed\u201d. This refers to the proteins that were commonly found in both experiments, regardless of concentration. The details of which are provided in Supplementary Table 3. &nbsp; The other sentence was also reworded for clarify \u201cTen unique <i>T. pallidum<\/i> proteins were found in the highest concentration (10 <sup>4<\/sup> bacteria\/ml) four in the enriched retentate sample (N = 10) and non-enriched sample (N = 10), two proteins detected were unique to either the enriched or unenriched samples (Figure 3).\u201d <b>2. Page 7, right column, paragraph 2.&nbsp; Tp47 is discussed twice in the paragraph with different gene names each time, ie, Tp47 (TP_0547) and Tp47 (TP_0574).<\/b> &nbsp; Thanks for pointing this out, this has been rectified to the actual ORF (TP_0574). <b>3. Page 3, Introduction, paragraph 1, line 1. \u201cT. pallidum, a non-culturable\u2026\u201d&nbsp; Suggest updating based on recent publication in mBio on culturing T. pallidum.<\/b> &nbsp; Good idea, this reference has now been added. <b>4. Figure 3. Please indicate the meaning of the asterisks on TP_0249, etc.<\/b> &nbsp; The asterisks refer to \u201c*-proteins selected as candidate biomarkers in this study.\u201d. This information has now been added","URL":"https:\/\/f1000research.com\/articles\/7-336\/v2#referee-comment-4031","order":2,"name":"referee-comment-4031","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by a grant from the Flanders Research Foundation, SOFI-B Grant (#757003) to CRK, http:\/\/www.fwo.be\/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}