Matt Padula

MASSyPupX: A FREE, open-source platform for off-site processing of shotgun DDA and DIA proteomics data.

✅ Runs on USB, PC, or server
✅ Pre-installed tools & libraries
✅ Perfect for education, collaboration & resource-limited labs

doi.org/10.1016/j.jp...
#Proteomics #DDA #DIA #Bioinformatics #FOSS

Why assume equilibrium? I have no evidence for or against that.

The thing I wonder about in these studies is that it implies that every microlitre of blood contains the same molecules at the same concentration as every other microlitre. That logic doesn't make sense to me.

I guess what I'm saying is that people are often driven by pursuit of wealth as a means of status. Cause how much money does one actually need.

Because the general public's definition of genius is someone who can do what they can't. Parting people with their money falls into this category, so billionaires are seen as geniuses.

There is a smaller intensity peak exactly 17 Da less (ammonia loss?) and a peak of similar intensity to that smaller peak at half its m/z. All 1+. None are on regular list of contaminants.

Joe Rogan gets universities better than a lot of university administrators.

Universities are supposed to be places where you tackle challenging ideas, and have your ideas challenged.

If you take that away, you don't have a university anymore. No matter what you put on your letterhead.

Those liking the post, have you seen this ion in your data?

I'm getting sick of editors and reviewers letting ridiculous terms like this through.

When analysing peptides from in-gel digests by LC-MS/MS, has anyone noticed a 1+ ion of m/z 1342.93 after washing the column with 80% ACN? We are leaving the pump at 80% ACN at 1uL/min for 5 mins after our usual 0-40% ACN gradient. Doesn't correspond to any contaminants. #massspechelp

When are you blokes writing the perspective on how "bad" things are? People keep talking about it but no one takes a stand and writes something.

‘Follow the mice’: How whistleblowers, secret lab videos brought down top scientist Staff were scared taking on the celebrated leader who’d won millions in government funding, but eventually, they had enough.

The fraud isn't the surprising bit. The fact that people were to scared to speak up. That's fucked. What kind of culture is that? Too bad it's common. www.smh.com.au/national/fol...

YouTube video by jidderbug2028 The_Goon_Show_-_What_Time_Is_It_Eccles__[www.keepvid.com].mp4

youtu.be/JrpnJo2fRt4?...

I need to remember this for our future collaborations. 🤔

Is there a hardware reason why this can't be done on older QE systems? The wording of MAP-MS got me excited that I could do it on one but it seems like it's only 480's and not even 120/240's.

It's a pre-print. One hopes those reviewing it for the journal it's been submitted to have the same view as you.

No. Simon Gerrans now with Matt Keenan and Bridie O'Donnell.

The Oz SBS crew are really good.

If it’s broke, nationalise it? Sadly, that’s broken thinking It’s back to the future: suddenly there’s a cry for government to step in whenever things fail. If only it was that easy.

www.smh.com.au/national/if-...

Want to see me rant about Bioinformatics related to Proteomics? Here's your chance.

UTS-USYD Bioinformatics Symposium 2025 - Fri 18 July. Green Theatre (Building 7, Level 2, Room 025) at UTS.
Register here: forms.gle/8CwyBjGAtBcF..., or the QR code in the flyer.

Jonas got found out today. This is going to be an interesting race.

Best read for the weekend.

Not with the continuation of the cap on numbers. They don't enter on merit but their ability to pay the fees.

Australia’s university system is ‘battered’ and ‘broken’ – a new book surveys the wreckage and offers some solutions Our universities require a major overhaul. Reform is possible, but only if a government is prepared to take up the challenge.

Aust Uni system is broke. Those in charge need to fix it or leave it to someone competent: theconversation.com/australias-u...

Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation - Nature Methods A quantitative mass spectrometry–based standard operating procedure to classify antibody performance in immunoprecipitation is assessed in a multilaboratory study.

www.nature.com/articles/nme...

Published 2015. This should have been earth shattering at the time and I reckon most never read it (I'm guilty).

This rate of validation suggests that affinity reagents such as antibodies should be considered non-specific until proven otherwise:

357 validated antibodies out of 1,124 tested.

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Another review/opinion piece about why studying proteoforms is important, this time when dealing with Anti-Microbial Resistance. Written by my super-talented PhD student @breyerwoodland.bsky.social with Piklu Roy Chowdhury and Matt O'Rourke.

doi.org/10.1016/j.ta...

[ASAP] Rapid Multi-Omics for Bacterial Identification Using Flow Injection–Ion Mobility–Mass Spectrometry Analytical ChemistryDOI: 10.1021/acs.analchem.5c00417

(ACS Anal Chem) [ASAP] Rapid Multi-Omics for Bacterial Identification Using Flow Injection–Ion Mobility–Mass Spectrometry: Analytical ChemistryDOI: 10.1021/acs.analchem.5c00417 #MassSpecRSS #ACSAChem