I'm the developer behind GoldenHaystack. Yes, I second Jenny -- please try it! www.goldenhaystack.org Pls email me directly (gsaxena@goldenhaystack.org) -- it should have no trouble with 1000s of DIA-MS files.

For over a decade, discovery MS proteomics algorithms only measured the ~5-25% of peptides that we users "knew about", while completely ignoring the remaining (and moreover invaluable) ~75-95% that was in the MS. A ~week ago, we published a preprint showing how we can go after that ~75-95%.

this ~75-95% set exclusively contains the unpredicted peptide sequences & unexpected PTMs that can be invaluable to your lab (e.g., please see reference to “Azheimer study” in first paragraph of page 3 of preprint and our website). We’re seeking labs that like to collaborate. (2/2)

Of those 4 limiting areas, do you have a super rough sense of how much each of those areas consumed in the total 4 week time frame?

Thanks for reading our paper, Vadim! I emailed you directly to set up a possible meet to interactively discuss the value of using SIL-search (which are by definition false matches, unlike using sequences from entrapment dbs etc.) Thanks in advance, Vadim. -Regards, Gautam.