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Although transcript fate can be measured by transcript abundance or translation efficiency, separating the contribution of individual cis\u2010element within a single transcript is an ongoing challenge. Current, massively parallel reporter assay (MPRA) approaches enable systematic interrogation of cis\u2010regulatory elements that control transcript stability, but translation\u2010focused MPRAs remain technically limited and often inaccessible. Here we present Nascent Peptide Translating Ribosome Affinity Purification (NaP\u2010TRAP), a reporter\u2010based approach that simultaneously measures translation and mRNA abundance. Unlike previous methods, NaP\u2010TRAP captures translation via immunoprecipitation of epitope\u2010tagged nascent peptide chains, providing instantaneous, frame\u2010specific readouts without specialized instrumentation. The method is scalable from single reporters to complex libraries, and adaptable across in vivo and in vitro systems. NaP\u2010TRAP is versatile, allowing assessment of cis\u2010regulatory impact of elements distributed throughout the mRNA, from cap\u2010to\u2010tail. This article covers experimental design, reporter construction, sample processing, and computational analysis for both low\u2010 and high\u2010throughput applications. Benchwork can be completed in 4 to 5 days, with quantitative polymerase chain reaction (qPCR)\u2010based readouts requiring only basic Microsoft Excel skills for data processing. Sequencing\u2010based readouts require command\u2010line and Python skills and add 2 to 3 days. NaP\u2010TRAP thus offers an accessible, robust, and quantitative platform to decode the regulatory logic of mRNA translation and stability in diverse biological contexts. \u00a9 2026 The Author(s).\n                    <jats:italic>Current Protocols<\/jats:italic>\n                    published by Wiley Periodicals LLC.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 1<\/jats:bold>\n                    : Design, assembly, and synthesis of NaP\u2010TRAP reporter libraries\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Support Protocol<\/jats:bold>\n                    : Design, assembly, and synthesis of NaP\u2010TRAP individual reporters and spike\u2010ins\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 2<\/jats:bold>\n                    : NaP\u2010TRAP delivery by micro\u2010injection in zebrafish embryos\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Alternate Protocol 1<\/jats:bold>\n                    : NaP\u2010TRAP delivery by transfection in cultured mammalian cells\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 3<\/jats:bold>\n                    : NaP\u2010TRAP pulldown and RNA extraction\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 4<\/jats:bold>\n                    : Preparation of NaP\u2010TRAP sequencing libraries\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Alternate Protocol 2<\/jats:bold>\n                    : NaP\u2010TRAP qPCR module for low\u2010cost validation\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 5<\/jats:bold>\n                    : Computational analysis of NaP\u2010TRAP MPRA data\n                  <\/jats:p>","DOI":"10.1002\/cpz1.70417","type":"journal-article","created":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T15:49:33Z","timestamp":1784130573000},"source":"Crossref","is-referenced-by-count":0,"title":["NaP\u2010TRAP: A Versatile and Accessible Workflow to Dissect Principles of Translational Regulation and mRNA Stability"],"prefix":"10.1002","volume":"6","author":[{"given":"Amit","family":"Gupta","sequence":"first","affiliation":[{"name":"Department of Genetics and Genome Sciences UConn Health  Farmington Connecticut"},{"name":"Binghamton University, State University of New York (SUNY)  Binghamton New York"},{"name":"These authors contributed equally to this work"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna Z.","family":"Struba","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genome Sciences UConn Health  Farmington Connecticut"},{"name":"These authors contributed equally to this 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