Park, Hana Yoon, Sung-Hyun Yu, Je-Wook Son, Jung hyun 2024-12-03T06:30:16Z 2024-12-03T06:30:16Z 2024-11-26 2024-11-22 https://pubs.kist.re.kr/handle/201004/151275 Protein identification by Nano liquid chromatography coupled to mass spectrometry (Nano LC-MS/MS) is a powerful technique widely used in proteomics to identify and profile proteins in complex biological samples. However, this approach often faces challenges when attempting to identify proteins with different isoforms or active forms, especially when using large, non-specific databases such as whole organism proteomes. This study highlights the critical importance of using curated FASTA files representing the active form of proteins, rather than whole organism databases, to achieve accurate protein identification. In our study, we attempted to match protein sequences for 14 specific proteins - Ercc6l2, Gdf15, IL-1b, IL-6, Myo18b, Peak1, Zfp113, Rb1cc1, Celsr2, Casp1, Akt1, Ceacam5, Cpne1, and Rsc1a1 - using their corresponding active form FASTA files. When querying the entire Mus musculus (mouse) proteome database, protein identification often failed due to the inclusion of inactive isoforms, precursor sequences, and redundant proteins. However, by focusing on FASTA files tailored to the active forms of these proteins, we significantly improved our identification success rate. These results highlight the need to use targeted, functionally relevant protein sequences to improve the precision of Nano LC-MS/MS analysis. Such strategies can improve both identification accuracy and sensitivity, thereby reducing false positives and increasing confidence in proteomic workflows. English 한국분석과학회 (The Korean Society of Analytical Sciences) Challenges in Protein Identification by LC-MS/MS and the need for Active Form-Specific FASTA files Conference 2 제73회 한국분석과학회 추계 학술대회 (The 73th Biannual Conference for The Korean Society of Analytical Sciences) 제73회 한국분석과학회 추계 학술대회 (The 73th Biannual Conference for The Korean Society of Analytical Sciences) KO 제주 부영호텔 2024-11-20 제73회 한국분석과학회 추계 학술대회