AbstractData‐independent‐acquisition mass spectrometry (DIA‐MS) is a state‐of‐the‐art proteomic technique for high‐throughput identification and quantification of peptides and proteins. Interpretation of DIA‐MS data relies on the use of a spectral library, which is optimally created from data acquired from the same samples in data‐dependent acquisition (DDA) mode. As DIA‐MS quantification relies on the spectral libraries, having a high‐quality, non‐redundant, and comprehensive spectral library is essential. This article describes the major steps for creating a high‐quality spectral library using a combination of multiple complementary search engines. We discuss appropriate strategies to control the false discovery rate for the final spectral library as a result of merging multiple searches. © 2021 The Authors Current Protocols © 2021 Wiley Periodicals LLC.This article was corrected on 25 July 2022. See the end of the full text for details.Basic Protocol 1: Searching DDA‐MS files with multiple search enginesBasic Protocol 2: Merging results from multiple search enginesBasic Protocol 3: Creating spectral libraries from merged resultsAlternate Protocol: Using CLI for automating tasksSupport Protocol: Creating concatenated FASTA files