The author of this blog has been applying mass spectrometry to riddles in biology for ...a while... First with clinical chemistry, then a PhD centered on glycopeptides before moving into the much less stressful worlds of messenger RNA, proteins and metabolites.
If you need help with any of these things, feel free to reach out to me directly: LCMSmethods@gmail.com. I'm one of those weird PIs who will do absolutely anything to make sure I'm still in the lab poorly pipetting and messing up my instruments.
When I'm not flooding the internet with unfiltered opinions on the coolest proteomics stuff - I'm an Assistant Professor at the brand new Organ Pathobiology and Therapeutics Institute (OPTIn) at the University of Pittsburgh! I have some other titles and affiliations, but that's already a lot to type. My team's sole focus is to use ultra-low input and single cell proteomics to tackle medical riddles that haven't been solved by other approaches. My team is just coming together in the summer of 2025 and we're getting a feel for the number of collaborations we can handle. Got a great idea? Please reach out!
Google Scholar has some more examples of what I and my teams do.
I also do stuff outside of proteomics - a side project I've been working on for years finally got to a good publishing point. If you want to feel like protein PTMs are a nice break, you should take a foray into the world of pesticide residue analysis. I didn't buy bulk aliquots of hundreds of different pesticides and develop methods to keep them to myself. More complete LCMS methods coming soon!
I was previously the chair of the US HUPO Virtual Media Outreach Group (now Educations and Outreach - which is a better name) and I'm still an active member. Being part of this team is one of the coolest things I've done in my career. Our goal is to make cutting edge proteomics technology more approachable. More information on US HUPO and VMO can be found here: https://www.ushupo.org/Committees
Thanks to VMO and US HUPO we got our first support (and guests) for Dr. Benjamin Neely and my other big time consuming outreach project - THE Proteomics Show Podcast series. While I was cleaning up this bio I looked and we're in Season 7 of the show with 85 episodes recorded? For some reason people keep listening so we'll keep doing it.
I am also the sole person responsible for selecting the official mascot for the US HUPO and HUPO organizations. It was the least I could do for organizations that have meant the absolute world to me the last several years.
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 other useful links:
www.LCMSmethods.org
ABRF Workflow Interest Network Panel. Honestly, I should probably take this down, but we had a great run as a team.
The Orsburn Lab Github. This isn't just the code that we've made, it's also other people's code that I use and you should too.
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: LCMS methods@gmail.com (remove the space)
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.
You can also find me on BlueSky - and I try to help answer questions on r/proteomics. I'm probably not one of the moderators. I'm pretty sure I'm not allowed to tell you if I am because of some Reddit rules.
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.
ReplyDeleteAwesome 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.
ReplyDeleteHi,
ReplyDeleteThanks 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!)
Great blog! Keep it going!!!
ReplyDeleteabsolutely!
DeleteHi Ben,
ReplyDeleteGreat Blog and How To Videos!
I wouldn't have believed reading about MS/proteomics could be fun. Thanks for showing me that it can.
ReplyDeleteBen, 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.
ReplyDeleteCheer!
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!
ReplyDeleteHi Ben,
ReplyDeleteI 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
Dear Ben,
ReplyDeleteWe 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
Surprised you never make mention of ASX: PIQ on the west coast of Australia?
ReplyDeleteI'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!!
DeleteHi Ben,
ReplyDeleteA quick question. Is PD2.1 a good tool for intact protein search? Thank you very much!
Eric
Ben,
ReplyDeleteI'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
Hey Ben;
ReplyDeleteHave 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
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.
DeleteDear Ben,
ReplyDeletesorry 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
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.
DeleteHi Ben,
ReplyDeleteI 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
Eric,
DeleteThey 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!
Hi Ben,
ReplyDeleteIs 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
Hi Ben,
ReplyDeleteI 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
Hello,
ReplyDeleteI 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.
Hi Ben,
ReplyDeleteJust 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
Hi Ben,
ReplyDeleteAny 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.
Enjoying your blog! Keep it up!
ReplyDeleteHi Ben,
ReplyDeleteDo 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!!!
Wait. Yes. I think so? Loading up PD 2.2 now. Nope, I don't see it...
DeleteHi Ben,
ReplyDeleteCan you please share with me a version of FTprograms that still has RecalOffline?
Thanks,
Hi There,
ReplyDeleteJust wanted to thank you for this cheerful attitude towards one of the hardest methodologies in biological sciences!