{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T12:53:39Z","timestamp":1790168019286,"version":"4.1.0"},"update-to":[{"DOI":"10.12688\/wellcomeopenres.17607.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T00:00:00Z","timestamp":1675209600000}}],"reference-count":16,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T00:00:00Z","timestamp":1675209600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["101842"],"award-info":[{"award-number":["101842"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns3:p>\n                    <ns3:bold>Background:<\/ns3:bold>\n                    <ns3:italic>Trypanosoma brucei<\/ns3:italic>\n                    is a protozoan parasite and etiological agent of human and animal African trypanosomiasis. It has a complex\n                    <ns3:italic\/>\n                    life cycle, but the most studied cellular types are the\n                    <ns3:italic>in vitro<\/ns3:italic>\n                    cultivated bloodstream- and procyclic-forms. These correspond to the replicating, mammalian host bloodstream-dwelling, slender trypomastigotes and tsetse vector midgut-dwelling procyclic lifecycle stages, respectively. Several proteomics studies have reported the differential abundance of proteins between these\n                    <ns3:italic>in vitro<\/ns3:italic>\n                    cultivated cell types. However, there are no datasets providing protein abundance, from most to least abundant, within and between both cell types.\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Methods:<\/ns3:bold>\n                    We used MaxQuant software 1.6.10.4 to reprocess a recent large-scale proteomics experiment from our laboratory and extracted intensity-based quantifications of the bloodstream and procyclic form proteomes.\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Results:<\/ns3:bold>\n                    We created a web interface to visually explore protein abundances within and between the\n                    <ns3:italic>in vitro<\/ns3:italic>\n                    cultivated\n                    <ns3:italic>T. brucei<\/ns3:italic>\n                    bloodstream and procyclic form proteomes.\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Conclusions:<\/ns3:bold>\n                    The protein abundance visualization tool, searchable by protein name(s) and attribute(s), is likely to be useful to the trypanosome research community. It will allow users to contextualise their proteins of interest in terms of their abundances in the\n                    <ns3:italic>T. brucei<\/ns3:italic>\n                    bloodstream and procyclic form proteomes.\n                  <\/ns3:p>","DOI":"10.12688\/wellcomeopenres.17607.2","type":"journal-article","created":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T12:30:06Z","timestamp":1675254606000},"page":"34","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":13,"title":["Visualisation of proteome-wide ordered protein abundances in Trypanosoma brucei"],"prefix":"10.12688","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0051-017X","authenticated-orcid":false,"given":"Michele","family":"Tinti","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael A. J.","family":"Ferguson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2023,2,1]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"231-45","DOI":"10.1016\/j.idc.2004.01.004","article-title":"History of sleeping sickness (African trypanosomiasis).","volume":"18","author":"F Cox","year":"2004","journal-title":"Infect Dis Clin North Am."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"e1005439","DOI":"10.1371\/journal.ppat.1005439","article-title":"Quantitative Proteomics Uncovers Novel Factors Involved in Developmental Differentiation of Trypanosoma brucei.","volume":"12","author":"M Dejung","year":"2016","journal-title":"PLoS Pathog."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"e36619","DOI":"10.1371\/journal.pone.0036619","article-title":"Comparative SILAC proteomic analysis of Trypanosoma brucei bloodstream and procyclic lifecycle stages.","volume":"7","author":"M Urbaniak","year":"2012","journal-title":"PLoS One."},{"key":"ref-4","doi-asserted-by":"publisher","first-page":"2233-44","DOI":"10.1021\/pr400086y","article-title":"Global quantitative SILAC phosphoproteomics reveals differential phosphorylation is widespread between the procyclic and bloodstream form lifecycle stages of Trypanosoma brucei.","volume":"12","author":"M Urbaniak","year":"2013","journal-title":"J Proteome Res."},{"key":"ref-5","doi-asserted-by":"publisher","first-page":"556","DOI":"10.1186\/1471-2164-13-556","article-title":"Proteome remodelling during development from blood to insect-form Trypanosoma brucei quantified by SILAC and mass spectrometry.","volume":"13","author":"K Gunasekera","year":"2012","journal-title":"BMC Genomics."},{"key":"ref-6","doi-asserted-by":"publisher","first-page":"152","DOI":"10.12688\/wellcomeopenres.15421.1","article-title":"Proteome turnover in the bloodstream and procyclic forms of Trypanosoma brucei measured by quantitative proteomics [version 1; peer review: 3 approved].","volume":"4","author":"M Tinti","year":"2019","journal-title":"Wellcome Open Res."},{"key":"ref-7","doi-asserted-by":"publisher","first-page":"337-42","DOI":"10.1038\/nature10098","article-title":"Global quantification of mammalian gene expression control.","volume":"473","author":"B Schwanh\u00e4usser","year":"2011","journal-title":"Nature."},{"key":"ref-8","doi-asserted-by":"publisher","first-page":"2301-2319","DOI":"10.1038\/nprot.2016.136","article-title":"The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.","volume":"11","author":"S Tyanova","year":"2016","journal-title":"Nat Protoc."},{"key":"ref-9","doi-asserted-by":"publisher","first-page":"D442-D450","DOI":"10.1093\/nar\/gky1106","article-title":"The PRIDE database and related tools and resources in 2019: improving support for quantification data.","volume":"47","author":"Y Perez-Riverol","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref-10","doi-asserted-by":"publisher","first-page":"D457-62","DOI":"10.1093\/nar\/gkp851","article-title":"TriTrypDB: a functional genomic resource for the Trypanosomatidae.","volume":"38","author":"M Aslett","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref-11","doi-asserted-by":"publisher","first-page":"376-86","DOI":"10.1074\/mcp.m200025-mcp200","article-title":"Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.","volume":"1","author":"S Ong","year":"2002","journal-title":"Mol Cell Proteomics."},{"key":"ref-12","doi-asserted-by":"publisher","first-page":"261-272","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: fundamental algorithms for scientific computing in Python.","volume":"17","author":"P Virtanen","year":"2020","journal-title":"Nat Methods."},{"key":"ref-13","doi-asserted-by":"publisher","first-page":"1034-1044","DOI":"10.1021\/pr401017h","article-title":"Accurate label-free protein quantitation with high- and low-resolution mass spectrometers.","volume":"13","author":"J Krey","year":"2014","journal-title":"J Proteome Res."},{"key":"ref-14","doi-asserted-by":"publisher","first-page":"62-72","DOI":"10.7171\/jbt.13-2402-003","article-title":"Optimization of data-dependent acquisition parameters for coupling high-speed separations with LC-MS\/MS for protein identifications.","volume":"24","author":"D Johnson","year":"2013","journal-title":"J Biomol Tech."},{"key":"ref-15","doi-asserted-by":"publisher","first-page":"51-59","DOI":"10.1016\/j.jprot.2019.03.005","article-title":"Label-free absolute protein quantification with data-independent acquisition.","volume":"200","author":"B He","year":"2019","journal-title":"J Proteomics."},{"key":"ref-16","article-title":"mtinti\/tbrucei_ibaq: v0.2 add zenodo.","author":"M Tinti","year":"2022","journal-title":"Zenodo."}],"container-title":["Wellcome Open Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-34\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-34\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-34\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T12:30:09Z","timestamp":1675254609000},"score":1,"resource":{"primary":{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-34\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,1]]},"references-count":16,"URL":"https:\/\/doi.org\/10.12688\/wellcomeopenres.17607.2","relation":{},"ISSN":["2398-502X"],"issn-type":[{"value":"2398-502X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,2,1]]},"assertion":[{"value":"Indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-34\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.19475.r48550, Vyacheslav Yurchenko, Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic, 08 Feb 2022, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-34\/v1#referee-response-48550","order":0,"name":"referee-response-48550","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Michele Tinti<\/b>; \n<i>Posted: 09 Feb 2022<\/i>; 1)Indeed, it is possible. We find it convenient to use this tool to visualise differential expression (RNA-seq) or abundance (proteomics) analysis using volcano and MA plots. However, creating a resource to display all the available data is beyond our reach. We will contact the TriTrypDB database and ask if they will consider implementing this visualisation for the datasets deposited there.&nbsp;  2)The 427 strain is commonly used for experiments in the lab, and the BES1 locus is available for the T. brucei 427 strain. However, &nbsp;the BES1 locus is absent in the sequenced genome of the T. brucei 927 strain that is commonly used for data analysis, as it provides a better gene annotation.&nbsp;  3)I tried the functionality in Firefox, Chrome and Safari using a mac laptop. I suspect it might be a windows system issue. I will do more tests to find the problem.  4)&nbsp;We will ask the publisher to change the links of the apps if possible. Unfortunately, I had to change the web hosting company after submitting the paper for an issue I didn't expect.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-34\/v2#referee-comment-4903","order":1,"name":"referee-comment-4903","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.19475.r48579, Stefan Magez, Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea, 01 Mar 2022, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-34\/v1#referee-response-48579","order":2,"name":"referee-response-48579","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Michele Tinti<\/b>; \n<i>Posted: 04 Mar 2022<\/i>; We indeed hope that this tool will be useful for the T. brucei community. We will add a mail contact to report issues with the application.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-34\/v2#referee-comment-4923","order":3,"name":"referee-comment-4923","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.19475.r48676, Kent L. Hill, Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA, 15 Mar 2022, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-34\/v1#referee-response-48676","order":4,"name":"referee-response-48676","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Michele Tinti<\/b>; \n<i>Posted: 24 Mar 2022<\/i>; We thank the reviewer for the feedback. I recently swiched the plots for coding reasons and I also added some new utilities. I will describe these changes in the next paper versions.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-34\/v2#referee-comment-4950","order":5,"name":"referee-comment-4950","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by Wellcome [101842; an Investigator award to M.A.J.F.]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":6,"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"}]}}