Wednesday, August 21, 2013

De Novo Assisted PTM "Blind Search" - PEAKS PTM

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.


25 comments:

  1. A haze meter measures the transparency; haze, see-through quality, and total transmittance of a material haze meter,

    ReplyDelete
  2. Thanks for sharing.I found a lot of interesting information here. A really very thankful and hopeful that you will write many more posts like this one. online b2b importers directory

    ReplyDelete
  3. Good day readers! Are you searching a company for writing essays or dissertation papers? So, this https://papernow.org/college-papers-for-sale agency is the best among writing agencies provider in the whole world for learners with the lowest prices. Essay is one of the mainly common forms of task writing. A part of your rating depends on general performance of your written papers. You have to prepare your articles within the deadline to obtain the highest points in your subjects!!!

    ReplyDelete
  4. The Department of Electronics & Communication Engineering, Our College is uptu colleges, Ghaziabad is organizing a Guest Lecture on the topic “Low Power Design Techniques in VLSI”. The lecture is scheduled for the students and faculty members of Electronics and Communication Engineering Alos top private mba colleges in delhi ncr.

    ReplyDelete
  5. This post isn't simply educational yet great too. The post is persuading to the point that it made a need to pick myassignmenthelp administrations.

    ReplyDelete
  6. Japan Tenders data comes from a number of private enterprises as well as government authorities. Tender are issued by Japan government departments, foreign financial organisations, and private businesses. Bidding Contracts issued by Multilateral Funding Agencies and Private Companies via Japan Government Departments. We are the largest bidding contractors and Tenders information service providers in the global market for Japan Tender and Bidding by staying up to date with all Japan Tenders details posted by Government departments or private firms in Japan for e-Procurement Businesses. BidDetail has a list of Japan Government Tenders.

    ReplyDelete
  7. Hello, wow I love this blog, such a important information, i like your writing skills and everything about this blog just caught my attention. Chinese b2b platform

    ReplyDelete
  8. This is an excellent post that is both informative and entertaining. I'm not sure why this hasn't occurred to other professionals in this subject. You need to keep on with your writing. I'm a student who aspires to be a fantastic writer, which I may do by ordering assignments, and I use online class services through https://www.buyessay.org.uk/write-my-essay/ to further my education.

    ReplyDelete
  9. Really nice and interesting post. I was looking for this kind of information and enjoyed reading this one. Keep posting. Thanks for sharing. for More Details Click Here:- Change AOL Mail Password

    ReplyDelete
  10. Awe some essay on education history, but nowadays most of the students feel online help so that they may easily complete their assignments that they could not fulfil for the final terms. coursework writing services

    ReplyDelete
  11. The professional assignment writing help is going second the data that predict that peak where we also can contribute with research

    ReplyDelete
  12. This comment has been removed by the author.

    ReplyDelete
  13. This is a fantastic article that is both educational and entertaining. I'm not sure why this hasn't occurred to other experts in this field. It is critical to keep writing. As a student who aspires to be a brilliant writer, I use online class services provided by homework help to further my education. Thanks for sharing with us.

    ReplyDelete
  14. If you want to play at the casino, you must choose the best. You can see here link by this.

    ReplyDelete
  15. This comment has been removed by the author.

    ReplyDelete
  16. our customers’ brands should also be known by their quality. Whether one is struggling with deciding the name of his business, typography, or the style logos. SEO experts

    ReplyDelete
  17. This is a fascinating and timely post. I appreciate you taking the time to write this. Continue your fantastic work! I hope to see more interesting factoids from your point of view in the future. Thank you so much for your assistance!
    protective order virginia code

    ReplyDelete
  18. Your blogs are really good and interesting. It is very great and informative. Then an in-house developed program will be used to assemble the de novo peptides into much longer sequences, protein contigs. In our experiments, the majority of assembled contigs had a length of 60~120 residues Bankruptcy lawyers in virginia. I got a lots of useful information in your blog. Keeps sharing more useful blogs..

    ReplyDelete
  19. Hey there, PeaksBlog! I just stumbled upon your article about the 'De Novo Assisted PTM Blind Search' and wanted to drop a line. First off, let me say how refreshing it is to find such a clear and concise breakdown of a rather complex topic. Your knack for simplifying intricate concepts without dumbing them down is truly impressive. I am here to aware those students who are looking for professional Dissertation Writing Services UK that we will help you in getting A+ Grades with 100% Guarantee.

    ReplyDelete
  20. Wow, the PEAKS PTM algorithm sounds groundbreaking! The integration of de novo sequencing for a "blind search" is ingenious—it must significantly enhance the efficiency of PTM identification. Reckless Driving New Jersey The focus on PTM rarity shows a thoughtful approach, reducing false assignments. This feature simplifies user input and streamlines the search process, making PEAKS 6 a game-changer for PTM analysis! abogado delitos sexuales nueva jersey

    ReplyDelete
  21. Flat rate credit card processing is a simplified pricing model for merchants, offering a straightforward fee structure. Unlike traditional interchange-plus pricing, flat rate processing charges a fixed percentage and a per-transaction fee for all card types. This streamlines cost calculations and benefits small businesses with predictable monthly expenses. While convenient, it may not be the most cost-effective for high-volume transactions or specific card types.

    Merchants should carefully evaluate their transaction patterns to determine if flat rate processing aligns with their business needs. Popular providers like offer flat rate options, attracting businesses seeking transparency in payment processing costs.

    ReplyDelete
  22. commercial contract disputes lawyer
    The '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.

    ReplyDelete
  23. 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.

    ReplyDelete
  24. This comment has been removed by the author.

    ReplyDelete
  25. "commercial truck accident lawyers"
    The 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