Wednesday, April 10, 2013

Why everyone should de novo?

When I was doing some house cleaning on old documents, I found a few slides created 5 years ago about why de novo sequencing should be included in all research workflows. Most of these things still stay true today and it aligns very well with PEAKS development. I'd like to share them here.

Problem:
“The organism I’m studying isn’t in any of the databases.”

Solution:
De novo sequencing is the only way to go.

Problem:
“I need more confidence in the peptides found by MS/MS ion search”

Solution:
Use an orthogonal approach like sequence tag searching or hybrid searching to validate the results

Problem:
“I can only explain <10% of my data. I need to boost my search engine’s performance.”

Solution:
Use two or more unique search engines. Then try de novo sequencing.

Problem:
“I think I’m still missing some peptides, maybe because of with PTM”

Solution:
Use de novo to find a partial sequence; matching this to a database will highlight peptides of interest.

Problem:
“I am still missing some peptides even after trying all PTM. But the data is great!”

Solution:
De novo + peptide homology search like SPIDER or BLAST.

Problem:
“My lab creates too much data for de novo sequencing”

Solution:
Use PEAKS. It’s fast enough.

36 comments:

  1. يتم رش جميع أنواع المبيدات الحشرية ، وتعمل الشركة على توفير الكثير من الأشياء التي يبحث عنها جميع العملاء باستمرار دون توقف عن العمل لأنها واحدة من أكثر الشركات التي يحتاجها جميع العملاء.
    شركة مكافحة حشرات

    ReplyDelete
  2. The Caribbean’s leading eLearning solutions CSEC Information Technology Ability Test provider, Powering regional Governments, Businesses, and Schools with our award-winning LMS and e-Courses.

    ReplyDelete
  3. Nervous about dieting for weight loss? Nutrition counseling can be fun and improve your health. Find out how our online Weight loss coach help.

    ReplyDelete
  4. Our Security Services in Texas Security Services in Texas are effective, affordable, and comprehensive. Don’t hold on until it’s too late, communicate with us now and enjoy all your requirements for security services handled speedily and effectively. Whatever your want, whatever kind of plot you keep or contend with, and whatever nature of services you need, GGS Security Services in Texas can always help you. We give experienced guards that can exist as needed.

    ReplyDelete
  5. TruGuard Security is a fully licensed and insured security services company led by law enforcement and ex-military professionals with extensive experience in the field. We employ uniformed security personnel who are well-trained to ensure that your site is kept safe at all times. We provide armed and unarmed Security Guard Services in Sacramento for many commercial industries and businesses, including restaurants, retail stores, and hotels.

    ReplyDelete
  6. Conveniently located in central Gallup, New Mexico, and Metairie, Louisiana our team understands the complex and challenging issues of family relationships and how changes within a family’s dynamic can Personal Injury Lawyer affect every area of each family members life Tribal Lawyer . Be they favourable or unfavourable changes or events, it is all part of the overall family dynamic.

    ReplyDelete
  7. We at Midori Aluminum have established a solid reputation for providing outstanding products and first-rate service to all of our consumers. Our founder comes from an engineering background where he places a strong emphasis on attention to detail, ensuring that each task is completed with the highest care. The versatility of our product range Aluminum Shopfront has propelled us to the forefront of design solutions for a diverse variety of difficult glazing projects.

    ReplyDelete
  8. How to Watch Ozark Season 4 Part 2 from Anywhere of the gripping thriller Ozark on April 29, 2022 solely on Netflix. Crime and drug thriller has always had something new for us. If you're looking for How to Watch Ozark Season 4 Part 2 from Anywhere in the world, keep reading because we've put up a comprehensive guide on how to do so.

    ReplyDelete
  9. RMHC of Norfolk is part of a global network of houses that provide housing for millions of families so they can stay close by their hospitalized child. The Ronald McDonald House offers ronald mcdonald house maryland a place to call home at little or no cost so families can afford the best care, regardless of location.

    ReplyDelete
  10. Completing Bridge's SEO campaign provides an all-in-one solution to SEO (on-page optimization, off-page optimization, and technical optimization) that ensures that your most valuable audience finds you online without you having to invest many hours in the process. With our revenue acceleration platform [url=http://completebridgesolutions.com/seo/]Seo Marketing Agency Near Me[/url] you can combine your SEO service plan with actionable revenue insights based on billions of data points and our decades of industry knowledge to generate more money for your business.

    ReplyDelete
  11. We review Timeshare Exit Companies helping you avoid scams. We provide detailed ratings and Newton Group Transfers reviews of 100's of exit companies.

    ReplyDelete
  12. Beyond the Box Nutrition takes great pride in ensuring that your experience is highly personalized, straightforward, Macro counting For weight loss, effective, and tailored to your specific needs and preferences. We believe that observing your existing habits, thoughts, and beliefs will increase your chances of success. Simply give us an overview of your goals, and we'll ensure to set you on the path toward success.

    ReplyDelete
  13. burn4privacy.com offers FREE NonVoip Burner-Numbers on which you can receive unlimited SMS live online Real Burner-Numbers. We only host REAL PREPAID SIM CARDS in combination with special software that allows our numbers to receive SMS WITHOUT ANY RESTRICTIONS, just like you can receive all kind of SMS on your smartphone. Please be aware that our free numbers and all messages received on them are PUBLICLY ACCESSIBLE. We also offer private numbers with exclusive access just for you. For private numbers, we only use BRAND NEW Prepaid Sim Cards, which are destroyed after the desired access period has expired. For all private numbers, you get 10 days access by default. However, an extension is always possible as long as you contact us before expiration of the access period. In case you have special needs, or you want to request bulk orders, please contact us at support@burn4privacy.com.

    ReplyDelete
  14. CabTime provides transportation services for our customers all throughout the United Kingdom. Our service providers have undergone a thorough evaluation. Each trip is closely monitored in real-time to ensure that clients receive the highest local standards and consistency, regardless of where their destination is. We provide Taxi Heathrow To Reading a complete range of passenger, executive, MPV people carriers, and chauffeur services at competitive rates.

    ReplyDelete
  15. We can inspect any floor area and test that it meets Australian Standards for safety. Slip Testing Sydney, Our technicians are highly trained and utilize the latest technology available including wet pendulum tests to ensure our clients have peace of mind and comply with their insurer’s requirements.

    ReplyDelete
  16. If your concern is to buy a camera for safety and protection then consider Dash Cam Man. Here you may find massive range of camera for vehicle Dash Cam 8k. So you may have the evidence of protection when you’re at road. It is a perfect solution to record reckless drivers.

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

    ReplyDelete
  18. Landlords may use our market analysis to make data-driven choices about their rental property, including rate predictions and other information that will allow them to invest and manage their investment property more effectively. Rental Properties Northwest Arkansas With our help, you can get an optimized rental value for your property. Fill out the form to get started with your FREE RENTAL PRICE ANALYSIS.

    ReplyDelete
  19. We can inspect any floor area and test that it meets Australian Standards for safety Slip Testing Brisbane. Our technicians are highly trained and utilize the latest technology available including wet pendulum tests to ensure our clients have peace of mind and comply with their insurer’s requirements.

    ReplyDelete
  20. RMHC of Norfolk is part of a global network of houses that provide housing for millions of families so they can stay close by their hospitalized child Non profits Virginia. The Ronald McDonald House offers a place to call home at little or no cost so families can afford the best care, regardless of location.

    ReplyDelete
  21. Communities deeply depend on our Unarmed Security Services for the protection of their homes, workplaces, schools, etc. People expect the security officers to take care of their personal properties and belongings and gatekeep the areas they live in from any potential threat. Furthermore, Our guards are required to be alerted and have immense strength to counter any danger there may be.

    ReplyDelete
  22. في عمليات تجميل وشد الوجه بالليزر يساعد على علاج التجاعيد والندوب وما إلى ذلك منفي مشاكل الوجه. تحتاج تقنية الليزر إلى حوالي ساعتين في مراكز عمليات تجميل الوجه في مصر حالة تجميل الوجه بالليزر بالكامل

    ReplyDelete
  23. The market is flooded with people looking to purchase with greater prudence. Amazon believes that Amazon believe we can aid people to do the same. Amazon Aware can be described as Shop You For available night dress set for womensin the United States, Canada, and Europe provides new products that are in fashion, home, cosmetics as well as home categories.

    ReplyDelete
  24. Your blog is great. I read a lot of interesting things from it. Thank you very much for sharing. Hope you will update more news in the future. for More Information Visit Here MCA Live Transfer Leads

    ReplyDelete
  25. Exciting entry! You offer a stunning assortment. Your article is interesting to read. Moreover. Here's where you can find out more about us and the work that we do: The operation of these Leads is simple. Lead generation executives are on the phone and emailing businesses all day to ensure they meet the criteria for an MCA Leads.

    ReplyDelete
  26. People count on the security guards to protect their private assets, keep their neighborhoods safe from outside threats, and guard their personal items. Furthermore, in order to combat any potential threats, Our guards must be very attentive and powerful. digimarketinginc.com

    ReplyDelete
  27. Nice interesting post. Problem and their solution are too good. You are intelligent to create this post. Thanks for sharing this good post. Keep sharing more interesting and informative blogs like this. Divorce Lawyers Arlington VA

    ReplyDelete
  28. Nice interesting post. Problem and their solution are too good. You are intelligent to create this post. Thanks for sharing this good post. calgary wealth management firms

    ReplyDelete
  29. People count on the security guards to protect their private assets, keep their neighborhoods safe from outside threats, and guard their personal items. Engineering & environmental solutions Ottawa

    ReplyDelete
  30. Caregivers in Florida are lifelines for the elderly and disabled, offering compassionate support. They ensure independence, provide companionship, and improve overall well-being. Their dedication is the heart of caregiving in the Sunshine State

    ReplyDelete
  31. This article was a game-changer for me! The insights into copywriting strategies were so practical and eye-opening. Can't wait to apply these tips to https://contentbaskit.com/unlocking-the-power-of-innocams-the-future-of-innovation/ my own writing. Thanks for sharing!

    ReplyDelete
  32. Great read! The tips on copywriting are super helpful. I especially liked the part about storytelling - it adds a whole new dimension to how I approach writing. Looking forward to book32 more insightful posts

    ReplyDelete
  33. The PEAKS Blog offers a diverse range of insightful content, blending narratives with articles, covering personal development, lifestyle, and trending issues. It provides quality and relevance, making it a commendable platform for inspiration and knowledge.Divorcio de Corte Suprema de Nueva York

    ReplyDelete
  34. A "de novo" mindset promotes continuous renewal, fostering personal and professional growth. It encourages adaptability, resilience, and learning, allowing individuals to break free from stagnant routines and embrace innovation. This journey benefits both individuals and the community. Summons With Notice Divorce New York

    ReplyDelete