Parag got many of us on board and made data accessibility a true community project. Involving labs like Dave Tabb's, companies like Insilicos, and our lab. We should be building on each others development efforts. From the start, Skyline has been part of the Proteowizard repo by design.

Not many realize how hard it was to get the six major instrument vendors to make their data files accessible. Parag definitely pushed for it early. When we ran into complexities of establishing a legal entity to sign the agreements, he established the Proteowizard Software Foundation.

That's great to know. Shocked that a fused silica emitter could contain this sort of bgrd. When we make our own column, the 'tip' is washed with methanol. Most of this is to remove the polyimide coating. Surprised a commercial vendor that makes an emitter doesn't have an extensive wash process.

Just be careful with what you wash your hands with. In general, if you can smell it, the mass spec can detect it. That old thread might have been from our lab. Michael Bereman was the one who caught the problem in our lab but was horrified when he traced it to his own deodorant.

We've experienced this only when there were selected deodorants or antiperspirants worn in the lab. I can assure you that Old Spice is a nightmare in an MS lab. We spent months tracking it down in the past. Here's the paper that gave us the idea to consider it. pubs.acs.org/doi/10.1021/...

Have you tried this from @willfondrie.comgithub.com/wfondrie/ppx

This is another argument for collecting all data by DIA. After the fact it's easy to extract 15 peptides in a targeted fashion. Likewise you can still search for unknowns.

For a limited set of proteins, we just target the expected peptides. It's not the search, it's which peptides are more quantitatively stable because of the protease protection.

Totally agree. Any antibody assay is fatally flawed by its use of an antibody.

I'm sure Thermo isn't thinking along these lines but who knows. Seems feasible to design the PEA amplification to produce peptide barcodes and use an IVTT step... tech Thermo has unique IP around.