In PEAKS 6, we have introduced a new algorithm for PTM "blind search", PEAKS PTM. This algorithm can search for modified peptides with all 600+ PTMs in the Unimod database. To use this algorithm, simply select the option in the PEAKS Search dialog.
How is the "blind search" achieved? The secret is de novo sequencing. In usual PTM search algorithm, all possible modification forms of all database peptides satisfying the enzyme digestion rules are tried to match the spectra.
In PEAKS PTM, we only search for PTMs on the peptides when there is a tag match*. The algorithm also takes the PTM rarity into account to reduce the search space and false PTM assignment.
With PEAKS PTM algorithm selected, users only need to specify a very small number of variable PTMs in de novo and PEAKS DB to speed up the search and rely on PEAKS PTM to find other modifications presented in the sample.
*X. Han et al. PeaksPTM: Mass Spectrometry Based Identification of Peptides with Unspecified Modifications. JPR 2011, 10(7): 2930-2936.
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ReplyDeleteThe 'Blind Search' feature in PEAKS PTM is a revolutionary tool for proteomics research, enabling the identification of post-translational modifications (PTMs) without prior knowledge. This feature has significantly enhanced the research workflow and provided valuable insights into protein modifications. The accuracy and efficiency of this tool have greatly improved PTM analysis, saving time and effort. The 'Blind Search' feature has revolutionized the way researchers approach PTM analysis by allowing them to explore unknown modifications. The software's ability to generate accurate and reliable results has been instrumental in advancing their research. The 'Blind Search' feature in PEAKS PTM is a remarkable tool for PTM analysis, offering a comprehensive and efficient approach to identifying unknown modifications, providing researchers with valuable insights into protein function. The user-friendly interface and robust algorithms make it a must-have for any proteomics researcher.
For those exploring advanced bioinformatics tools, it's worth noting that the Delta Executor platform offers an innovative approach to de novo assisted PTM blind search, enhancing the accuracy and efficiency of proteomics research.
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ReplyDeleteThe article introduces the De Novo Assisted PTM 'Blind Search' feature in PEAKS PTM, highlighting its functionality and significance in peptide analysis. It explains how it helps identify post-translational modifications, enhancing protein modification understanding. The article suggests incorporating real-world examples to showcase the feature's effectiveness, and user testimonials to highlight its impact on researchers. A brief conclusion summarizing the key benefits and implications of the feature would provide a strong wrap-up, reinforcing the tool's significance.
ReplyDelete"Blind Search" by De Novo Assisted PTM, part of the PEAKS PTM platform, revolutionizes protein analysis with its innovative approach. This cutting-edge tool combines advanced algorithms with user-friendly interfaces, enabling researchers to uncover hidden insights in proteomic data effortlessly. With its unparalleled accuracy and efficiency, Blind Search streamlines the identification of post-translational modifications, paving the way for groundbreaking discoveries in proteomics research. Get ready to unlock new dimensions of protein analysis with Blind Search.
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The De Novo Assisted PTM "Blind Search" - PEAKS PTM is an impressive feature for proteomics research, offering powerful capabilities for identifying post-translational modifications (PTMs) without prior assumptions. By combining de novo sequencing with advanced algorithms, the tool efficiently detects unexpected or novel PTMs, significantly expanding the scope of protein analysis. Its ability to provide accurate and detailed results makes it a valuable asset for uncovering complex biological processes
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