William Stafford Noble

[William Stafford Noble @thabangh]

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

[William Stafford Noble @thabangh]

@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 (https://t.co/eNGs1nK5W9).

[William Stafford Noble @thabangh]

@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 (https://t.co/asiefz7oRz). That paper also suggests how to deal with neighbors (peptides that share parts of their theoretical spectra).

[William Stafford Noble @thabangh]

@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.

[William Stafford Noble @thabangh]

@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?

[William Stafford Noble @thabangh]

@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.” https://t.co/Dju6myudpm

[Will Fondrie @wfondrie]

Interested in de novo peptide sequencing from #massspec #proteomics data? Check out our latest #preprint about Casanovo!

👉 https://t.co/gz7bgTIYpS

That's right folks - it's time for another #tweetorial 🧵 (1/9)

[Melih Yilmaz @melih__yilmaz]

Want to learn more about the state of the art in de novo peptide sequencing at #ASMS2023?

Come check out our:
- Evening workshop #17 for a Casanovo tutorial on Monday
- Talk at the AI session on Wednesday
#TeamMassSpec

[William Stafford Noble @thabangh]

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

[UW Genome Sciences @uwgenome]

Congratulations to Lincoln Harris on being awarded an NRSA fellowship!

[William Stafford Noble @thabangh]

Casanova is the new state of the art in de novo peptide sequencing. https://t.co/nRtetnavmf

[Ran Zhang @zhangran12]

Check out Polarbear🐻‍❄️, a method to predict the missing scATAC-seq profiles just based on scRNA-seq, and vice versa. 🐻‍❄️ also derives matching in between scRNA-seq and scATAC-seq profiles, enabling integration of different types of single cell measurements. https://t.co/JiCpGSakyh

[Lilian Heil @lilian_heil]

Our paper about building spectral libraries from DIA data is officially out @JProteomeRes! Thank you to everyone who worked on this and to our reviewers for their feedback, I'm very excited about the final product.

[Andy Lin @andy_compbio]

Obligatory post following a bioRxiv submission. In this work we show that 1) PSM-level FDR estimates in practice are invalid and 2) a simple variant of the peptide-level FDR estimate protocol can yield a significantly greater number of peptide detections

[Nature Reviews Genetics @NatureRevGenet]

Our featured article: Navigating the pitfalls of applying machine learning in genomics https://t.co/rrHhjqOWPp #Review by @seawhalen, @jmschreiber91, William S. Noble & Katherine S. Pollard @GladstoneInst @Stanford @UW
@uwgenome @UCSF @czbiohub

[William Stafford Noble @thabangh]

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. https://t.co/phyjf8VWKt

[Andy Lin @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 score, MS1Connect, that measures the similarity between pairs of mass spectrometry runs solely using MS1 scans and without any peptide identifications. 🧵 1/9

[William Stafford Noble @thabangh]

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

[William Stafford Noble @thabangh]

Excited for another 5 years of studying genome 3D architecture! https://t.co/lch3O64Ipb