{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T22:19:04Z","timestamp":1762899544617,"version":"3.37.3"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2018,3,30]],"date-time":"2018-03-30T00:00:00Z","timestamp":1522368000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"International Science & Technology Cooperation Program of China","award":["2014DFB30010","2014DFA33160","2012DFB30080"],"award-info":[{"award-number":["2014DFB30010","2014DFA33160","2012DFB30080"]}]},{"name":"National Program on Key Basic Research Project","award":["2014CBA02000","2012CB910300"],"award-info":[{"award-number":["2014CBA02000","2012CB910300"]}]},{"name":"National Key Research and Development Program of China","award":["2017YFA0505102","2017YFC0908404"],"award-info":[{"award-number":["2017YFA0505102","2017YFC0908404"]}]},{"name":"National High-tech R&D Program of China","award":["2012AA020201"],"award-info":[{"award-number":["2012AA020201"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31200582","31170779","31200992","31270822","31770886","31700682"],"award-info":[{"award-number":["31200582","31170779","31200992","31270822","31770886","31700682"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004826","name":"Beijing Natural Science Foundation","doi-asserted-by":"publisher","award":["5132012","Z131100005213003"],"award-info":[{"award-number":["5132012","Z131100005213003"]}],"id":[{"id":"10.13039\/501100004826","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Science and Technology Major Project","award":["2017SHZDZX01"],"award-info":[{"award-number":["2017SHZDZX01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Mass spectrometry (MS) based quantification of proteins\/peptides has become a powerful tool in biological research with high sensitivity and throughput. The accuracy of quantification, however, has been problematic as not all peptides are suitable for quantification. Several methods and tools have been developed to identify peptides that response well in mass spectrometry and they are mainly based on predictive models, and rarely consider the linearity of the response curve, limiting the accuracy and applicability of the methods. An alternative solution is to select empirically superior peptides that offer satisfactory MS response intensity and linearity in a wide dynamic range of peptide concentration.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We constructed a reference database for proteome quantification based on experimental mass spectrum response curves. The intensity and dynamic range of over 2 647 773 transitions from 121 318 peptides were obtained from a set of dilution experiments, covering 11 040 gene products. These transitions and peptides were evaluated and presented in a database named SCRIPT-MAP. We showed that the best-responder (BR) peptide approach for quantification based on SCRIPT-MAP database is robust, repeatable and accurate in proteome-scale protein quantification. This study provides a reference database as well as a peptides\/transitions selection method for quantitative proteomics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SCRIPT-MAP database is available at http:\/\/www.firmiana.org\/responders\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty201","type":"journal-article","created":{"date-parts":[[2018,3,29]],"date-time":"2018-03-29T11:09:01Z","timestamp":1522321741000},"page":"2766-2772","source":"Crossref","is-referenced-by-count":2,"title":["A reference peptide database for proteome quantification based on experimental mass spectrum response curves"],"prefix":"10.1093","volume":"34","author":[{"given":"Wanlin","family":"Liu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lai","family":"Wei","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianan","family":"Sun","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinwen","family":"Feng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gaigai","family":"Guo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lizhu","family":"Liang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tianyi","family":"Fu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingwei","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yin","family":"Huang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weimin","family":"Zhu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bei","family":"Zhen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"},{"name":"Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chen","family":"Ding","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China"},{"name":"State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan 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