About Ben Orsburn


I received my Ph.D. in Biology from Virginia Tech, mostly by doing MS-based small molecule elucidation and quantification, with a little bit of proteomics and targeted metabolomics.  Afterward I did 2 short post-docs, at JHU and NCI, before taking a Staff Scientist position at the NIAID.  I did a bunch of weird stuff for a while -- including just flying out to hang out it in all sorts of mass spec labs all over the world -- before finding my way back to about where I started.

My postdoc work dealt with investigating the mechanism of action of chemotherapeutics slated for clinical trials via genomics and proteomics.  Since this would leave very few opportunities to publish, I started this blog in order to stay current and attempt to stay relevant in some way to the field.  It still hasn't seemed like a bad idea, so I've never stopped.

2018 has been a huge year for me. I was able to return to research as part of Thorkell Andresson's  team at the Advanced Technology Research Facility where we endeavor to support the research of all researchers at the NCI's Center for Cancer Research.

In April of 2018, www.LCMSmethods.Org came online. With the amazing team of Editors and Contributors on this project, we are working to help standardize all methods in mass spectrometry and to lower the boundary between biology and getting good mass spectrometry data. Optimization takes a lot of time in a new application. If you can just go and get an instrument method already optimized by an expert -- your uptime increases and so does the quality of your data.  Stay tuned. I couldn't be more proud to be the lead on this project and team and our first real methods release is shaping up to be something incredible.

In May, I was elected to the ABRF Workflow Interest Network Panel. The mission of WIN is to help scientists and resource facilities improve reproducibility of scientific data by optimizing analytical parameters and providing recommendations for reproducible inter-laboratory workflows. With a mission this big, it's going to be a lot of work. If you'd like to contribute definitely reach out to the Panel or to me -- we've got big plans for what mass spectrometry can be -- and with your help we can do it.

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: I really am this enthusiastic about this field all the time.

24 comments:

  1. ManojMay 7, 2014 at 1:44 AM

    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.

    ReplyDelete
  2. Hongbo GuoJune 20, 2014 at 1:04 PM

    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.

    ReplyDelete
  3. BenJune 20, 2014 at 4:05 PM

    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!)

    ReplyDelete
  4. AnonymousAugust 12, 2014 at 9:01 AM

    Great blog! Keep it going!!!

    ReplyDelete
  5. Naomi DiazJanuary 16, 2015 at 8:29 AM

    Hi Ben,

    Great Blog and How To Videos!

    ReplyDelete
  6. Bill BreuerJanuary 17, 2015 at 6:10 AM

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

    ReplyDelete
  7. Alejandro CohenApril 17, 2015 at 12:33 PM

    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!

    ReplyDelete
  8. BenJune 8, 2015 at 10:45 AM

    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!

    ReplyDelete
  9. Targeted ProteomicsJuly 27, 2015 at 4:02 AM

    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

    ReplyDelete
  10. AnonymousApril 8, 2016 at 1:51 AM

    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

    ReplyDelete
  11. AnonymousJuly 26, 2016 at 11:23 PM

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

    ReplyDelete
    Replies
    1. BenAugust 1, 2016 at 2:28 PM

      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!!

      Delete
  12. Eric Chuanlong CuiSeptember 13, 2016 at 11:29 AM

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

    Eric

    ReplyDelete
  13. cphaneufSeptember 23, 2016 at 5:54 PM

    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

    ReplyDelete
  14. AnonymousMarch 15, 2017 at 2:37 PM

    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

    ReplyDelete
    Replies
    1. BenMarch 17, 2017 at 4:23 AM

      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.

      Delete
  15. Marc SMarch 24, 2017 at 7:43 AM

    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

    ReplyDelete
    Replies
    1. BenMarch 28, 2017 at 12:52 PM

      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.

      Delete
  16. Eric Chuanlong CuiSeptember 22, 2017 at 2:48 PM

    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

    ReplyDelete
    Replies
    1. BenSeptember 25, 2017 at 4:45 PM

      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!

      Delete
  17. AnisMarch 27, 2018 at 7:30 AM

    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

    ReplyDelete
  18. AnisMarch 27, 2018 at 7:32 AM

    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

    ReplyDelete
  19. B.BJuly 10, 2018 at 11:39 PM

    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.

    ReplyDelete

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