I am deleting my Twitter account. Please follow me on BlueSky (@wnoble.bsky.social).

@pwilmarth @neely615 @andy_compbio @Smith_Chem_Wisc Not sure if this is what you are referring to when mentioning PTMs, but we recently also showed that PTMs don’t seem to significantly affect the validity of FDR control in narrow search, as had been previously suggested (.

@pwilmarth @neely615 @andy_compbio @Smith_Chem_Wisc We recently pointed out some of the issues with searching with variable modifications and how to counter that in your FDR analysis (. That paper also suggests how to deal with neighbors (peptides that share parts of their theoretical spectra).

@pwilmarth @neely615 @andy_compbio @Smith_Chem_Wisc The idea behind TDC is that an incorrect match is equally likely to hit the target or the decoy database. This requires special care in constructing decoys. We don't recommend the reversing the proteins; rather, one should reverse or shuffle the peptides.

@pwilmarth @neely615 @andy_compbio @Smith_Chem_Wisc It sounds like you believe target/decoy FDR estimation has a liberal bias because it doesn't take into account some types of errors.  This is not a bound in the statistical sense.  What are the "non-random sources of peptide sequencing errors" and why are they biased?

@pwilmarth @neely615 @andy_compbio @Smith_Chem_Wisc FDR is defined as the expected rate of false discoveries. So it’s a mean rather than an upper or lower bound. If you want an upper bound, please see our recent JPR tutorial on “Bridging the false discovery gap.”

RT @wfondrie: Interested in de novo peptide sequencing from #massspec #proteomics data? Check out our latest #preprint about Casanovo! 👉 h…

RT @melih__yilmaz: Want to learn more about the state of the art in de novo peptide sequencing at #ASMS2023? Come check out our: - Evening…

@Smith_Chem_Wisc @neely615 Friends don’t let friends control FDR at the PSM level.

RT @oligopain: Excited to introduce Tigerfish—a computational ecosystem for the design of interval-specific oligo probes targeting repetiti…

RT @uwgenome: Congratulations to Lincoln Harris on being awarded an NRSA fellowship!

Casanova is the new state of the art in de novo peptide sequencing.

RT @zhangran12: Check out Polarbear🐻‍❄️, a method to predict the missing scATAC-seq profiles just based on scRNA-seq, and vice versa. 🐻‍❄️…

RT @lilian_heil: Our paper about building spectral libraries from DIA data is officially out @JProteomeRes! Thank you to everyone who worke…

RT @andy_compbio: Obligatory post following a bioRxiv submission. In this work we show that 1) PSM-level FDR estimates in practice are inva…

RT @NatureRevGenet: Our featured article: Navigating the pitfalls of applying machine learning in genomics #Review…

The state of the art in de novo peptide sequencing has just advanced: meet Casanovo, a transformer model that translates from the sequence of peaks in a spectrum to the sequence of amino acids in a peptide.

RT @andy_compbio: Not going to lie. Part of the reason I created an account was to promote this preprint of mine. We have created a new sc…

@NorSivaeb @nesvilab Thanks, Ron. Not sure I'd call these "edge cases." But sticktoitiveness is what we're aiming for!