About Ben Orsburn


The author of this blog has been applying mass spectrometry toward trying to solve biological problems for nearly half his life, now as junior faculty in the Bumpus lab at the Johns Hopkins School of Medicine. Watch out, we've got an amazing team here and big plans. 

This blog is a symptom of an obsession with the power of mass spectrometry and the belief that these technologies, when used to their potential, will make the world a better place.

Some useful links: 
www.LCMSmethods.Org We're trying to make mass spectrometry more approachable to non-experts by providing solid validated methods for as many applications as we can. 

ABRF Workflow Interest Network Panel. Our chosen mission at WIN is to help scientists and resource facilities improve reproducibility of scientific data by optimizing full workflows. We could definitely need your help! 

Someone reminded me recently that my Github might be a useful thing to link here. You'll find forks to lots of the cool stuff I use and talk about here.

If you'd like to reach me, the best way is to place a comment on the blog post of interest, or send me a direct email:  orsburn@vt.edu

Fair warning, though: If I appear enthusiastic about this stuff in these blog posts, you haven't seen me wound up in person. I love this stuff. 

29 comments:

  1. Hi Osburn, your videos are quite useful. I have worked with small molecules since last 17 years and now learning Bio-smilar and a bit of proteomics application. Can you tell me how to identify which compounds have gone through neutral loass and the respected neutral loss in chromatogram.

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  2. Awesome blog and video. I tried to get some info for intact protein using QE and found your blog. May ask you more about if in the future. BTW, why you set up blog using .ca? which make me think that you are in Canada.

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  3. Hi,
    Thanks for you comments. The blog is up on blogger.com, but it is mirrored on blogger.ca as well as 13 other countries, I think. I think it saves bandwidth for Google or something (and they really run this thing, I just write the words in the boxes!)

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  4. Great blog! Keep it going!!!

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  5. Hi Ben,

    Great Blog and How To Videos!

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  6. I wouldn't have believed reading about MS/proteomics could be fun. Thanks for showing me that it can.

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  7. Ben, just stumbled upon your blog... what a nice surprise! so many questions I have asked myself in many years, all condensed into one blog! I'll keep track of this blog... and throw you some (trivial) questions whenever I can.
    Cheer!

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  8. Thanks for all the positive feedback, everybody! Its great to do something I enjoy and for other people to somehow get something out of it!

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  9. Hi Ben,

    I noticed you (re)tweeted a few videos that we put up on youtube from our recent Targeted Proteomics Course (http://targetedproteomics.ethz.ch/) hosted by the Aebersold group in Zurich. There is a now a youtube playlist which has all 21 video lectures from this course in the correct order:

    https://goo.gl/nr89LK

    Maybe you readers would be intersted in hearing about it? Nice blog by the way!

    All the best,
    Ben Collins

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  10. Dear Ben,

    We made this great video about proteomics for the Hecklab in Utrecht. Maybe you would like to share it. https://www.youtube.com/watch?v=1G6jTGAfgUc

    Thanks,

    Caspar

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  11. Surprised you never make mention of ASX: PIQ on the west coast of Australia?

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    Replies
    1. I'd never heard of it until you wrote this! Where did this come from? How are they doing all that stuff with MALDI...? I will investigate! Thanks!!

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  12. Hi Ben,
    A quick question. Is PD2.1 a good tool for intact protein search? Thank you very much!

    Eric

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  13. Ben,
    I'm trying to figure out how the label free node/workflow for PD 2.1 calculates protein abundance from peptides? Can you point me in the right direction?
    Thanks,
    Cliff Phaneuf

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  14. Hey Ben;
    Have you seen the Thermo ASMS 2016 Poster "A simplified approach to fast and accurate, high throughput targeted MS2 quantitation using internal standards" by Eliuk and McAlister

    It shows a really cool method on Lumos that uses a HRAM triggered MS2 IT Y1 narrow mass range scans that then triggers full mass range OT-HCD MS2 for heavy and a mass shifted quad offset to get an OT-HCD MS2 scan for the endogenous peptide. Unfortunately they use a Lua piece of in-house software Xcalibur-Workbench by M.Senko..Have you seen this software in your travels? Any suggestions who I could talk to? I have collected data and used Skyline but I need to be able to get the full scan OT-MSMS data separated from the IT-MS2 data

    Thanks

    Darryl

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    1. I can only think of 2 Darryl's smart enough to write this comment. If you didn't just get an email about this topic from me, shoot me a line (orsburn@vt.edu). I think I can help.

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  15. Dear Ben,
    sorry to spoil the party. But if you are Ben Orsburn whose Researchgate profile says „Thermo Fisher Scientific
    Proteomics Unit” then this is quite relevant to this blog. Why not be honest about this? Or have you retired recently („These days -- I'm a hobbyist scientist. I do global proteomics and untargeted metabolomics mostly for fun.“)?
    Otherwise a very interesting blog.
    Marc

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    1. Glad you like the blog! ResearchGate isn't up-to-date, I really don't do science as a job anymore, just for fun. I also like to make it abundantly clear that this blog and my employer are very separate entities. This is just a weird hobby and is definitely not endorsed by my employer in any way.

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  16. Hi Ben,
    I remembered you have some videos showing how to use QE in this blog. But I cannot find it. Did you get it down from the blog? Thank you.
    Eric

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    1. Eric,
      They are still up somewhere. If you go to Vimeo.com and type in "Q Exactive" you'll find my videos and some other useful ones!

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  17. Hi Ben,

    Is it possible to tell me where to download the nodes for PD 2.2
    I need the RT-Aligner ,Xlinkx search, and the Spectrum Files RC

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  18. Hi Ben,

    I hope you are doing well.
    Is it possible to help me to download the nodes for PD 2.2 RT-Aligner and MSPepSearch, PMI Byonic, PMI preview, Spectrum Files RC, Xlinkx search please

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  19. Hello,
    I am coming into microbiology lab to do proteomics with zero experience in MS but huge courage to learn everything even alone. I am so so glad to found your blog, which explains things in the language I can understand (the course i've taken was all about philosophy lol). I got that feeling that your blog will be with me throughout this journey. Wish me luck and please keep posting.

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  20. Hi Ben,
    Just to let you know that I added the RSS feed of your blog to my lab website at https://www.proteomicscenter.nl/. Keep up the good work!
    Cheers,
    Jeroen

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  21. Hi Ben,
    Any updates on the Boxcar/Boxfahrt optimization you were doing on the Fusion 1, do you have any news to discuss them, we were trying to optimize it as well and we appreciate your help and input.

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  22. Enjoying your blog! Keep it up!

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  23. Hi Ben,
    Do you know if PD 2.2 still calculate emPAI? We use it with PD 2.1 but we can not find it in 2.2.
    Thanks!!!

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    Replies
    1. Wait. Yes. I think so? Loading up PD 2.2 now. Nope, I don't see it...

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