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Nick Riley

@nmriley.bsky.social
1.3K followers 622 following 178 posts

Assistant Professor, University of Washington, Dept. of Chemistry. PI of the Riley Research Group, @riley-research.bsky.social. Glyco, mass spec, chembio. Sports, food, travel, dogs. riley-research.com

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Nick Riley @nmriley.bsky.social · 12/09/2026
Are you requiring certain combos or signal for them? Just one or two without signal thresholding can lead to over assumption of glyco signal, but it is a tricky balance of how to not be too strict. In the end though, as you said, not an end-all-be-all, just a way to get a snapshot of possibilities
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Nick Riley @nmriley.bsky.social · 12/09/2026
I think your oxonium strategy is the way to go. It’s what we do before database searching, too. Including much else turns into a full glyco search (or limits/biases you too much) from my view… I was just curious is you had figured out a smarter way than me!
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Nick Riley @nmriley.bsky.social · 11/09/2026
This is interesting! I haven’t had a chance to look under the hood yet, but what went into calling the glycopeptide candidate spectra? Delta masses of a few glycans, oxonium ions, combo of both?
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Nick Riley @nmriley.bsky.social · 28/08/2026
Overall, PTCR proves once again to be a useful gas-phase reaction that enables us to simplify our spectra to see the complexity of glycoproteoforms. We are excited to keep exploring this technology to better understand glycoproteoforom landscapes and use that to connect glyco regulation to function.
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Nick Riley @nmriley.bsky.social · 28/08/2026
We then took a deeper dive into our EpCAM data to look at what integrating bottom-up glycopeptide and intact glycoproteoform measurements can get us, and @emmajays.bsky.social helped us use @glycoshape.org to model how a glycoproteoform with two occupied N-glycosites might look like.
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Nick Riley @nmriley.bsky.social · 28/08/2026
We applied this workflow to characterize four glycoproteins well-described translational interests: EpCAM, TIGIT, CD40, PDL1, and CD24. For each of these, we can show multiple delta masses between glycoproteoforms that show expected glycan compositions that explain different glycan heterogeneity.
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Nick Riley @nmriley.bsky.social · 28/08/2026
One challenge was that tools traditionally used for low Rp spectra were not satisfactorily deconvolving our high Rp spectra that had isotopic resolution. @timveth.bsky.social developed a new workflow handle hRp-DIA-PTCR data, including software packages called PTsliCR and IsoTrac (both @ our GitHub)
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Nick Riley @nmriley.bsky.social · 28/08/2026
We found that collecting DIA-PTCR spectra with high resolving powers (Rp) provided significant benefits. Prior work had focused on low Rp data collection (which can limit glycoproteoform assignments), so we describe our method as high resolving power (hRp)-DIA-PTCR to help emphasize this benefit.
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Nick Riley @nmriley.bsky.social · 28/08/2026
Here is an example from EpCAM, where we can assign discrete glycoproteoform identities.
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Nick Riley @nmriley.bsky.social · 28/08/2026
We used DIA-PTCR to simplify overlapping glycoproteoform signals into resolvable species. Integrating this with bottom-up glycopeptide and direct mass technology (DMT) measurements lets us describe glycoproteoforms with site-specific insight.
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Nick Riley @nmriley.bsky.social · 28/08/2026
Glycoproteoforms are the unit of biological information in the glycoproteome, but measuring intact glycoproteins to capture combinatorial modification states remains a huge #glycotime challenge. @timveth.bsky.social tackled this issue head on in the latest preprint from @riley-research.bsky.social
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Lucy Dornan @lucygdornan.bsky.social · 26/06/2026
Leaving Blackburn after a really wonderful week discussing all things Golgi and glycobiology! So many new things learned and ideas to be explored - it’s an excellent time to have a thesis discussion to write..!
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Iain Wilson @iainwilsonwien.bsky.social · 25/06/2026
Nick Riley @nmriley.bsky.social is just starting his @biochemsoc.bsky.social Early Career Research Award Lecture during the 95th Harden Conference! #glycotime #TeamMassSpec
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Jay Forsythe @jaygforsythe.bsky.social · 19/06/2026
“The project of freedom, Juneteenth reminds us, is precarious, and we should regularly remind ourselves how many people who came before us never got to experience it, and how many people there are still waiting.” - Clint Smith, How the Word Is Passed
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Christopher Rose @cmichaelrose.bsky.social · 03/06/2026
Writing from the airport. Sad to miss it, but out preprint just dropped in time! Have a great discussion tonight! www.biorxiv.org/content/10.6...
biorxiv.org
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Nick Riley @nmriley.bsky.social · 02/06/2026
If you are looking for a Tuesday evening #ASMS2026 workshop to attend, consider joining us for fun discussions about real time mass spectrometry.
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Riley Research Group @riley-research.bsky.social · 01/06/2026
The Riley Research Group is excited to be at #ASMS2026. There will be a lot of cool science this week, and we hope to add to the conversation with presentations from our group!
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Mark McIntyre @markjmcintyre.bsky.social · 03/04/2026
I don't remember seeing an image of Earth before that captures the (thin, fragile, tiny layer of) atmosphere so clearly. I mean, look at that.
Zooming in on the photo of Earth taken by astronauts on Artemis II on their way to the Moon, you can clearly see the Aurora Borealis and thin layer of atmosphere wrapping around the planet.Zooming in on the photo of Earth taken by astronauts on Artemis II, you can clearly see the thin layer of atmosphere wrapping around the entire planet.
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Devin Schweppe @dschweppe.bsky.social · 07/04/2026
The next iteration of O-MAP targeting genomic loci is now at eLife!! DNA O-MAP enables proximity labeling at specific DNA loci took a ton of work from many lab members and collaborators, so it's really exciting to wrap up this paper with @oligopain.bsky.social! elifesciences.org/articles/102...
elifesciences.org
DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci
DNA O-MAP enables proximity labeling at specific genomic loci in fixed cells using programmable oligonucleotides, revealing locus-proximal proteomes and chromatin interactions without genetic modifica...
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B. Erin Cole @berincole.bsky.social · 07/04/2026
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Nick Riley @nmriley.bsky.social · 02/04/2026
Check out her other work here: www.impactmedianw.com
impactmedianw.com
N. G. BOECK
HELLO! (Are you looking for M. Nicole Nazzaro? You found me! My professional byline changed in April 2025, but everything else is staying the same: email, phone, website URL, etc. Welcome!) WHAT I...
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Nick Riley @nmriley.bsky.social · 02/04/2026
(Disclaimer: I was not involved with this article, but Nicole and I have had a lot of great conversations since she took my Quantitative Analysis course, so I am a bit biased!)
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Nick Riley @nmriley.bsky.social · 02/04/2026
Her background as a bona fide journalist w/ career pivot back into science and research makes her writing on science/the scientific enterprise particularly interesting. This topic about managing failure and fostering perseverance is evergreen in science. Thanks for adding to this dialogue, Nicole!
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Nick Riley @nmriley.bsky.social · 02/04/2026
It is very cool to see this piece from a former student of mine, @mnicolen.bsky.social, in Nature's Career Feature section: www.nature.com/articles/d41...
nature.com
My PhD student is stuck. How do I teach them perseverance and problem solving?
A new principal investigator wants to help PhD students to develop resilience and creativity in the laboratory without hovering or doing the work for them.
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Nick Riley @nmriley.bsky.social · 27/03/2026
A big congratulations to the 2026 I. M. Kolthoff Award Winners! acsanalytical.org/2026/03/12/2... This @acs.org award for undergraduate researchers supported 4 outstanding students (Damon Chan, Alex Szczepankiewicz, Katelyn Barnes, & Zane Alsebai) attending @pittcon.bsky.social and #ACSspring 2026
acsanalytical.org
2026 I. M. Kolthoff Award Winners
The I.M. Kolthoff Award is given annually to deserving undergraduates who have done undergraduate research in the field of analytical chemistry, broadly defined, in celebration of the life and accompl...
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Nick Riley @nmriley.bsky.social · 30/03/2026
We plan to highlight a new analytical chemist each quarter in the Division Newsletter. If you are interested in nominating someone to be highlighted, please enter their information here: docs.google.com/forms/d/e/1F...
docs.google.com
Meet an Analytical Chemist Suggestion Form
American Chemical Society Division of Analytical Chemistry Education Committee is sponsoring a new initiative called "Meet an Analytical Chemist" where we highlight a scientist from our community once...
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Nick Riley @nmriley.bsky.social · 30/03/2026
Check out the newest entry in the ACS Div. of Analytical Chem. Education Committee's "Meet an Analytical Chemist" initiative. This quarter we highlight Dr. Christina Jones, Partnerships and Outreach Strategist at NIST: acsanalytical.org/2026/02/26/m...
acsanalytical.org
Meet an Analytical Chemist – February 2026
Christina Jones, Ph.D.National Institute of Standards and Technology, Office of Advanced Manufacturing, Partnerships and Outreach Strategist How did you get started in the field of Analytical Chemistr...
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Nick Riley @nmriley.bsky.social · 27/03/2026
A big congratulations to the 2026 I. M. Kolthoff Award Winners! acsanalytical.org/2026/03/12/2... This @acs.org award for undergraduate researchers supported 4 outstanding students (Damon Chan, Alex Szczepankiewicz, Katelyn Barnes, & Zane Alsebai) attending @pittcon.bsky.social and #ACSspring 2026
acsanalytical.org
2026 I. M. Kolthoff Award Winners
The I.M. Kolthoff Award is given annually to deserving undergraduates who have done undergraduate research in the field of analytical chemistry, broadly defined, in celebration of the life and accompl...
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 26/03/2026
Fantastic new resource for glycoproteomics from @nmriley.bsky.social and coworkers #glycotime
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Nick Riley @nmriley.bsky.social · 26/03/2026
As always, we appreciate authors like Rebeca and Morten (and many in our field) who make raw data publicly available. Data sharing streamlines #glycotime tool building and helps us advance together as a field.
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bioRxivpreprint @biorxivpreprint.bsky.social · 25/03/2026
Mucin-binding protein shuttles enable delivery of brain-targeted therapeutics www.biorxiv.org/content/10.64898/20…
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Nick Riley @nmriley.bsky.social · 25/03/2026
In all, GlycoDiveR is meant to improve accessibility of glycoproteomic-specific analyses and lower the barrier to exploring biological narratives embedded in rich glycoproteomic datasets. We hope it can be useful for your #glycotime work. Try it out here: github.com/riley-resear...
github.com
GitHub - riley-research/GlycoDiveR
Contribute to riley-research/GlycoDiveR development by creating an account on GitHub.
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Nick Riley @nmriley.bsky.social · 25/03/2026
These figures are a sampling of GlycoDiveR's >25 customizable functions & publication-quality visualizations, each accessible with a single line of code. Its modular architecture can accommodate new analyses from us and others, and we plan to update it with new visualizations regularly.
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Nick Riley @nmriley.bsky.social · 25/03/2026
Once glycoproteins of interest are pinpointed via glycoproteome-scale analyses, GlycoDiveR also generates glycosite-level analyses for indiv proteins. This includes site maps w/ heterogeneity differences b/t conditions, a quant heat map for all glycosites, and glycan comparisons for indiv glycosites
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Nick Riley @nmriley.bsky.social · 25/03/2026
Importing data w/ GlycoDiveR automatically connects to the @glycosmos.bsky.social API to provide GlyTouCan accession numbers for glycopeptides, and it connects to the #uniprot API to pull in associated protein annotations to assess, for example, which BP, CC, or MF are associated with glycopeptides.
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Nick Riley @nmriley.bsky.social · 25/03/2026
Glycoprotein-Glycan (GPG) bipartite networks have been adopted by several groups as way to "fingerprint" the glycoproteome when viewing an entire dataset. They can also be filtered to show how specific glycan features are distributed across the glycoproteome or differ between conditions.
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Nick Riley @nmriley.bsky.social · 25/03/2026
Classic visualizations for differential expression, like volcano plots, are available, and subsets of glycopeptides can be further processed to look for trends, such as glycan categories more represented in up- or down-regulated species. Glycoprotein rank plots can also show abundance shifts.
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Nick Riley @nmriley.bsky.social · 25/03/2026
GlycoDiveR generates Venn digrams and UpSet plots to compare overlap in glycopeptides, glycoproteins, glycosites, and glycans between two groups or large sets of groups. Glycan vs. Glycosite scatter plots can identify potentially interesting glycoproteins with high or low glycan microheterogeneity.
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Nick Riley @nmriley.bsky.social · 25/03/2026
For glycoproteome-scale analyses, visualizing data completeness and filtering for desired numbers of quantitated species per condition are functions our group uses often. Look at where in the LC-MS/MS gradient glycopeptides eluted can help with data assessment and experiment iterations, too.
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Nick Riley @nmriley.bsky.social · 25/03/2026
GlycoDiveR makes data normalization easy to perform and assess, including loadings plots for PCA. A single line of code generates other data quality assessments (w filtering capabilities), too, including identification bar graphs, peptide length distributions, m/z error trends, and CV distributions.
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Nick Riley @nmriley.bsky.social · 25/03/2026
GlycoDiveR is an open-source, modular R framework with >25 customizable glycoproteome- and glycosite-scale visualizations that can be generated with minimal programming expertise. We reanalyzed data from Kawahara et al. to demonstrate GlycoDiveR's features: www.mcponline.org/article/S153...
mcponline.org
HEXB Drives Raised Paucimannosylation in Colorectal Cancer and Stratifies Patient Risk
In BriefAiming to find glyco-markers against colorectal cancer (CRC), we applied systems glycobiology to CRC patient specimens. Multiomics data revealed that noncanonical paucimannosidic proteins form...
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Nick Riley @nmriley.bsky.social · 25/03/2026
The complexity of glycoproteomics data creates a bottleneck in data interpretation and communication. We (@timveth.bsky.social, @riley-research.bsky.social) built GlycoDiveR as a step toward bridging gaps between search-engine output and biological interpretation through #glycotime visualizations.
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PastelBio @pastelbio.bsky.social · 25/03/2026
GlycoDiveR: a modular R framework to analyze and visualize highly dimensional glycoproteomics data www.biorxiv.org/cont... --- #proteomics #prot-preprint
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 13/03/2026
Exciting new discovery from @jimwellsucsf.bsky.social and coworkers, a new class of potential cancer antigens flipped onto the cell surface via autophagy-associated exocytosis, featuring first author and former PhD student Corleone Delaveris! #proudofalumni
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Nick Riley @nmriley.bsky.social · 05/03/2026
We are generally limited by long accumulation times, so we try to keep it to as few scans per precursor as possible. But sometimes multiple scans can be the only answer, depending on what you need!
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Elisa Fadda @elisafadda.bsky.social · 02/03/2026
Wee thread 🧵⬇️ on our new #glycotime with @siglecdude.bsky.social John Klassen and @glycocode.bsky.social 🥳 where we show Siglecs as molecular precision tools, able to recognise sialylated glycans with surgical precision in their natural environment, not bad for a lectin! 😎 doi.org/10.1038/s420...
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Nick Riley @nmriley.bsky.social · 27/02/2026
This was a relatively straightforward set of experiments we approached from a tutorial-like perspective. Hopefully it can be useful for folks interested in #glycotime that have not thought much about MS/MS scan ranges before. Check out the publication here: pubs.acs.org/doi/10.1021/... 10/10
pubs.acs.org
Understanding m/z Range Settings for MS/MS Scans: A Case Study with Intact Glycopeptides
Effective glycopeptide identification with tandem mass spectrometry (MS/MS) often relies on both low mass-to-charge (m/z) ions derived from glycan-specific oxonium ions and higher m/z peptide fragment...
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Nick Riley @nmriley.bsky.social · 27/02/2026
are geared toward the fragment ions you care about. For glycoproteomics, adhering to typical scan range guidelines can unnecessarily exclude valuable low or high m/z fragment ions. We recommend larger scan ranges (120-3600 m/z) that capture informative ion types without signal loss. 9/10
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Nick Riley @nmriley.bsky.social · 27/02/2026
The take home message: paying attention to MS/MS scan settings like scan range is important, especially for complex biomolecules like glycopeptides. Following guidelines that generally work in proteomics can be detrimental for modified peptides, and it is worth checking that your methods... 8/10
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Nick Riley @nmriley.bsky.social · 27/02/2026
There is a limit to how large scan ranges can be before ion loss. We saw that 120-3600 m/z was fine, while 100-3600 m/z and 120-4000 m/z started to show signal loss. This goes back to ion motion in RF devices, as governed by Mathieu equations (i.e., q-values that describe stable trajectories). 7/10
The number of detected MS/MS ions was compared for EThcD scans using five different mass ranges. The ions were binned in 100 m/z bins and presented as the median per 10 scans.
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