{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T01:38:17Z","timestamp":1789436297177,"version":"build-2803163510"},"reference-count":68,"publisher":"SAGE Publications","issue":"8","license":[{"start":{"date-parts":[[2014,8,1]],"date-time":"2014-08-01T00:00:00Z","timestamp":1406851200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["OMICS: A Journal of Integrative Biology"],"published-print":{"date-parts":[[2014,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Among the neglected tropical diseases, leishmaniasis is one of the most devastating, resulting in significant mortality and contributing to nearly 2 million disability-adjusted life years. Cutaneous leishmaniasis is a debilitating disorder caused by the kinetoplastid protozoan parasite\n                    <jats:italic toggle=\"yes\">Leishmania major<\/jats:italic>\n                    , which results in disfiguration and scars.\n                    <jats:italic toggle=\"yes\">L. major<\/jats:italic>\n                    genome was the first to be sequenced within the genus\n                    <jats:italic toggle=\"yes\">Leishmania<\/jats:italic>\n                    . Use of proteomic data for annotating genomes is a complementary approach to conventional genome annotation approaches and is referred to as proteogenomics. We have used a proteogenomics-based approach to map the proteome of\n                    <jats:italic toggle=\"yes\">L. major<\/jats:italic>\n                    and also annotate its genome. In this study, we searched\n                    <jats:italic toggle=\"yes\">L. major<\/jats:italic>\n                    promastigote proteomic data against the annotated\n                    <jats:italic toggle=\"yes\">L. major<\/jats:italic>\n                    protein database. Additionally, we searched the proteomic data against six-frame translated\n                    <jats:italic toggle=\"yes\">L. major<\/jats:italic>\n                    genome. In all, we identified 3613 proteins in\n                    <jats:italic toggle=\"yes\">L. major<\/jats:italic>\n                    promastigotes, which covered 43% of its proteome. We also identified 26 genome search-specific peptides, which led to the identification of three novel genes previously not identified in\n                    <jats:italic toggle=\"yes\">L. major<\/jats:italic>\n                    . We also corrected the annotation of N-termini of 15 genes, which resulted in extension of their protein products. We have validated our proteogenomics findings by RT-PCR and sequencing. In addition, our study resulted in identification of 266 N-terminally acetylated peptides in\n                    <jats:italic toggle=\"yes\">L. major<\/jats:italic>\n                    , one of the largest acetylated peptide datasets thus far in\n                    <jats:italic toggle=\"yes\">Leishmania<\/jats:italic>\n                    . This dataset should be a valuable resource to researchers focusing on neglected tropical diseases.\n                  <\/jats:p>","DOI":"10.1089\/omi.2013.0159","type":"journal-article","created":{"date-parts":[[2014,6,17]],"date-time":"2014-06-17T16:27:42Z","timestamp":1403022462000},"page":"499-512","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":42,"title":["Neglected Tropical Diseases and Omics Science: Proteogenomics Analysis of the Promastigote Stage of\n                    <i>Leishmania major<\/i>\n                    Parasite"],"prefix":"10.1177","volume":"18","author":[{"given":"Harsh","family":"Pawar","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]},{"name":"Rajiv Gandhi University of Health Sciences","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Santosh","family":"Renuse","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]},{"name":"Amrita Vishwa Vidyapeetham","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sweta N.","family":"Khobragade","sequence":"additional","affiliation":[{"name":"National Centre for Cell Sciences","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandip","family":"Chavan","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]},{"name":"Manipal University","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gajanan","family":"Sathe","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]},{"name":"Manipal University","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Praveen","family":"Kumar","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kiran N.","family":"Mahale","sequence":"additional","affiliation":[{"name":"National Centre for Cell Sciences","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kalpita","family":"Gore","sequence":"additional","affiliation":[{"name":"National Centre for Cell Sciences","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aditi","family":"Kulkarni","sequence":"additional","affiliation":[{"name":"National Centre for Cell Sciences","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanwi","family":"Dixit","sequence":"additional","affiliation":[{"name":"National Centre for Cell Sciences","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rajesh","family":"Raju","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T. S. Keshava","family":"Prasad","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H. 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