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Poster Presentations
Day 4, June 25（Wed.）
Room P (Maesato East, Foyer, Ocean Wing)
- 4P-PM-38
Spectra-Sum Method for Protein Quantification from LC-MS/MS and TMT labeling Data
(1KBSI, 2UST-KBSI, 3CDDC Research Center)
oHeeyoun Hwang1,2, Hahyun Lee1,3, Geul Bang1, Jin Young Kim1,3
There are two methods used to calculate data for protein quantification using LC-MS/MS with TMT labeling. Spectra-sum method is calculated as a sum of the intensities of TMT report ions in spectra level. In other hand, Spectra-ratio method is calculated as a median of the ratio intensities with the global reference ion. In order to find a best quantification method, we prepared Hela standard peptides with TMT-6-plex labeling of difference protein content ratio as 0.5:0.5:1.0:1.0:2.0:2.0. First, we identified 3,684 proteins with FDR < 1% as spectra and global protein level using Integrated Proteomic Pipeline and ProteinInferencer. Of 30 replicated experiment of day by day, 16,384 is median number of identified spectra. We calculated the ratio value between the different protein content samples using the TMT reporter ions. A spectra-sum method resulted in 87% of proteins with coefficient variance (CV) < 30% and 0.07 standard deviation (SD). The other hand, in a spectra-ratio method, 45% proteins have CV less than 30% and 0.11 SD. It is indicated that spectra-sum method is more accurate quantification for a greater number of proteins. This method was applied to the large scaled proteomic data of bile duct cancer (n = 208).
This study was supported by the Korea Institute of Marine Science & Technology Promotion (Grant no. RS-2024-00405273)