We were not aware of Triqler and will compare it. One difference is rhat we use protein intensities while triqler uses peptides.
@mengchun.bsky.social can you add to that?

- as expected, quantitation at very low amounts (250 pg) is substantially worse than at "normal" loading. This will have implications on single cell proteomics.

Have a read!

4/4

- as standard for most of us, applying a 1.5-fold cut off (representing a 2-3x sigma) limits false discoveries.

- there seem to be instrument and method dependent differences in how many points per peak are necessary for good quantitation.

- be cautious with "atypical" proteomics expts where a large number of proteins change.

- the most important factor for filtering proteins to get very good quantitation is the number of quantified peptides.

- that being said, "single peptide wonders" are still surprisingly well quantified.

3/4

Using various ratios of a two and three-proteome mix enabled us to do several controlled quantitative experiments (CQEs).

They are in our experience essential to test novel DIA methods.

We identified a few recommendations such as:

2/4

This Friday.

unfortunately, I feel that the people from the latter group are the ones that shoot down grants (and papers) because in their mind we only generate "lists".

However, these lists are hugely important for communities and just because they don't appreciate them, doesn't mean they are not useful.

thank you!

I had expected many fewer people. Glad to see that it does not affect the conference too much!

Woohoo, congratulations, Tanmay! Well deserved!