GSE112623 Optimal settings of mass spectrometry open search strategy for higher confidence

Contributors : Shaohua Lu ; Zhibiao MaiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMore than half of the mass spectra could not be identified in most proteome mass spectrometry experiments. Various modifications have been considered as a major reason. Open search strategy was then introduced to solve this problem, however, lacking thorough quality assessment using independent information. Here, we used the “Suspicious Discovery Rate (SDR)” based on the translatome sequencing (RNC-seq) as an independent source to assess the proteome open search strategy. We found that the open search strategy increased the spectra utilization with the cost of increasing suspicious identifications that lacks transla tion evidence. We further suggested that restricting the peptide FDR below 0.1% would efficiently control the suspicious identifications of open search methods and enhanced the confidence of the peptide identification with modifications than the narrow window search. These results facilitated the pr oper use of open search methods for higher quality of proteome identifications with the information of post-translational modifications and single amino acid polymorphisms

Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research