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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 · 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 · 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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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
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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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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Nick Riley @nmriley.bsky.social · 27/02/2026
In general, we could get away with larger scan ranges (120-3600 m/z) without much loss in low or high m/z signal. This large scan range captured low m/z oxonium ions and higher m/z glycan-retaining peptide fragments, which could not be fully captured by adhering to scan range suggestions. 5/10
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Nick Riley @nmriley.bsky.social · 27/02/2026
A general rule of thumb uses multiples of the first m/z value to guide what scan range can be used to effectively transmit ions. Following these guidelines, however, limits the scan range and excludes useful ion types generated from glycopeptides, especially with electron-based fragmentation. 3/10
A representative spectrum shows increased oxonium ion and higher mass-to-charge fragment coverage upon breaking the 5–10–15 rule
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Nick Riley @nmriley.bsky.social · 27/02/2026
MS/MS scan range can be an afterthought that doesn't receive attention in method design, but improper settings can affect experimental outcomes. This is especially true in glycoproteomics. A #glycotime thread about a new #JASMS paper on this idea from @riley-research.bsky.social 1/10
The mass range of tandem mass spectra can be categorized into three main regions. For glycopeptides, the lower mass range contains mainly oxonium ions, the middle range contains mainly peptide fragments, and the high range contains charge-reduced fragments. All regions contain valuable fragment ion information, but they can only be simultaneously accessed by breaking the 5–10–15 rule.
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Nick Riley @nmriley.bsky.social · 10/11/2025
Not only did Kayla do a great job with her #HUPO2025 presentation, but she also was recognized this afternoon as one of the winners of the competitive 2025 Quantitative Proteomics Grant from Thermo Fisher Scientific. Way to go, Kayla!
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Nick Riley @nmriley.bsky.social · 09/11/2025
If you are at #HUPO2025 and want to see some recent work from @riley-research.bsky.social, come check out Kayla’s talk on Monday afternoon in the Glycoproteomics session in the Frontenac Ballroom! My poster on our recent work informatics tools is on Monday afternoon too. See you there! #glycotime
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Nick Riley @nmriley.bsky.social · 24/09/2025
NP enrichment also helped O-glycopeptide characterization, but MAX enrichment was less beneficial. We looked into CSF, too. We think this is one of the first applications of Seer's NPs to CSF, so we did proteomics and glycoproteomics. Be sure to check out the pre-print if this sounds interesting!
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Nick Riley @nmriley.bsky.social · 24/09/2025
It's rare that a single LC-MS/MS can provide IDs for all glycopeptides in a mixture, so we ran enrich enrichment multiple times on the instrument. This allowed us to capture as much of the population of glycopeptides that we could -- an important thing when exploring how enrichment methods differ!
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Nick Riley @nmriley.bsky.social · 24/09/2025
Large dynamic range in biofluids is an issue for glycoproteomics just like with proteomics. We saw that Seer's NP mixtures (A and B) combined with MAX enrichment provided a boost in N-glycopeptide IDs relative to no nanoparticles (NP0), with the majority of IDs being unique to the NP enrichments.
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Nick Riley @nmriley.bsky.social · 23/07/2025
@riley-research.bsky.social had a great time catching up with local research at the Cascadia Proteomics Symposium last week. The lineup featured talks from Katie Kothlow and Haley Schramm, and a lightning talk/poster from @emmajays.bsky.social Congrats to Emmajay for her 2nd-place poster award too!
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Nick Riley @nmriley.bsky.social · 02/06/2025
#ASMS2025 offers great evening workshops. If you are interested in real-time decision-making during MS data acquisition or still looking for one to join, consider the Real time Mass Spectrometry Workshop featuring speakers and panelists Sarah Sipe, Aarthie Senathirajah, and Manuel Peris Diaz.
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Nick Riley @nmriley.bsky.social · 02/06/2025
On Tuesday, our poster presentations include work from @timveth.bsky.social, Katie Kothlow, and @vishnutejus.bsky.social. Vishnu just gave a great presentation during the undergraduate poster competition tonight, too! On Thursday, Dr. Haley Schramm will present a poster and I will give a talk.
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Nick Riley @nmriley.bsky.social · 02/06/2025
On Monday, our poster presentations include work from Kayla Markuson, @jacobrussell02.bsky.social, Ruby Zhang, Dr. @emmajays.bsky.social, and Anna Duboff.
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Nick Riley @nmriley.bsky.social · 02/06/2025
@riley-research.bsky.social is excited for #ASMS2025 in Baltimore! We made sure to capitalize on some of the classics, like a crab dinner at LP Steamers and an Orioles game, before the conference festivities kicked off. Come hear what we have been up to!
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Nick Riley @nmriley.bsky.social · 17/04/2025
Welcome! You picked a great week to be here. Don’t forget to check out the views up on main campus if you can. Took these on my walks to/from work this week
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Nick Riley @nmriley.bsky.social · 16/04/2025
We heard of an interest in tutorial style manuscripts, so we (@timveth.bsky.social, Katie Kothlow) took an opportunity to explore the implications for glycopeptide analysis of the "5-10-15" rule of thumb used to set the m/z range for tandem MS. A pre-print is here: chemrxiv.org/engage/chemr...
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Nick Riley @nmriley.bsky.social · 26/03/2025
Here is a screenshot of the poster about GlyCounter I am presenting at this week's Glycobiology Gordon Research Conference to give you an overview of analyses we include in the pre-print.
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Nick Riley @nmriley.bsky.social · 23/03/2025
Finally, congratulations to the newly elected 2027 GRS Co-Chairs, Andrew Alexander and @lornamilne.bsky.social! Looking forward to the great meeting you plan in CA. Overall, it was a group of impressive group of early career researchers from 14+ countries. The future of #glycotome is in good hands
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Nick Riley @nmriley.bsky.social · 23/03/2025
Congratulations to our poster winners, Eva Maria Stork and Lorenzo Rossi! Also congratulations to poster honorable mention presentations from Taryn Lucas, Katrin Nuẞbaumer, Til Schlotter, Sandhya Sridhar, Natalie Stewart, Bożena Szulc!
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Nick Riley @nmriley.bsky.social · 23/03/2025
A big thank you to @docgatordawg1.bsky.social, Stacy Malaker, @elisafadda.bsky.social, @glycocode.bsky.social, and @glyco.me for participating in our GRS Mentorship Session on Careers in Glycoscience.
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Nick Riley @nmriley.bsky.social · 23/03/2025
The Glycobiology Gordon Research Seminar this weekend was a great kickoff to the Glyco GRC this week. ~70 grad students and postdocs shared awesome #glycotime data and built community. Much appreciation is owed to my co-chair @fionachembot.bsky.social who played a big role in its success.
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Nick Riley @nmriley.bsky.social · 07/03/2025
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Nick Riley @nmriley.bsky.social · 02/03/2025
Highlights from our week include: Travel awards for Katie (graduate) and @vishnutejus.bsky.social (undergraduate) 🎉 Poster presentations by @emmajays.bsky.social y.social, Haley, Vishnu, and me. We had fun with our poster lightning talks, too! 1st place overall poster award to Katie! 🎉
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Nick Riley @nmriley.bsky.social · 02/03/2025
Despite current events, @riley-research.bsky.social enjoyed @us-hupo.bsky.social last week! Connecting w/ colleagues was an antidote for the frustration that occupies a lot of my brain space these days Thanks for the continual motivation to pursue good science and support scientists however we can
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Nick Riley @nmriley.bsky.social · 01/03/2025
The Stand Up for Science rally has been scheduled for March 7th from 12-3PM at Seattle Center (by the mural amphitheater).
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Nick Riley @nmriley.bsky.social · 10/02/2025
We updated our @riley-research.bsky.social website this weekend, including a new section on our Useful Links page that consolidates materials we found helpful in the current events discourse, re: funding cuts. Hopefully it can be a helpful resource: www.riley-research.com/useful-links
A screenshot of useful links on the Riley Research Group's website for understanding F&A costs and other current events with research funding.
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Nick Riley @nmriley.bsky.social · 31/01/2025
Actual picture from a @riley-research.bsky.social group meeting this week
Iteration on a popular cartoon meme showing a weary man saying "What a year, huh" and a colleague replying, "Captain, it's January."
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Nick Riley @nmriley.bsky.social · 22/12/2023
Ruby Zhang joins the RRG as a 1st-year graduate student. Growing up in Los Angeles, CA, Ruby was previously at UC-San Diego, Pfizer, and CalTech before coming to UW. Welcome, Ruby! Read more here: riley-research.com/group-member...
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Nick Riley @nmriley.bsky.social · 22/12/2023
Jacob Russell joins the RRG as a 1st-year graduate student. From Columbus, OH, Jacob was previously at the Ohio State University and the Olesik lab before coming to UW. Welcome, Jacob! Read more here: riley-research.com/group-member...
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Nick Riley @nmriley.bsky.social · 22/12/2023
Kayla Markuson joins the RRG as a 1st-year graduate student. From the Minneapolis, MN area, Kayla was previously at Drake University and Eurofins Scientific before coming to UW. Welcome, Kayla! Read more here: riley-research.com/group-member...
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Nick Riley @nmriley.bsky.social · 22/12/2023
Katie Kothlow joins the RRG as a 1st-year graduate student. From the St. Paul, MN area, Katie was previously at UW-Madison and the Coon lab before coming to UW. Welcome, Katie! Read more here: riley-research.com/group-member...
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Nick Riley @nmriley.bsky.social · 22/12/2023
Anna Duboff joins the RRG as a 1st-year graduate student. From the Boston area, Anna was previously at Boston University, in the Peace Corps, and at Codiak BioSciences before coming to UW for a summer rotation with us. Welcome, Anna! Read more here: riley-research.com/group-member...
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Nick Riley @nmriley.bsky.social · 22/12/2023
Dr. Tim Veth arrived at UW in October, joining as our second postdoc! Tim earned his Ph.D. with the Heck and Altelaar labs at Utrecht University, and then made his way to join us in the PNW. Welcome, Tim! riley-research.com/group-member...
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Nick Riley @nmriley.bsky.social · 22/12/2023
Dr. Emmajay Sutherland joined as a postdoc in September, our first official lab member! From Scotland, she earned her Ph.D. with the Czekster group at the University of St. Andrew's before joining us here in Seattle. Welcome, Emmajay! riley-research.com/group-member...
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Nick Riley @nmriley.bsky.social · 17/11/2023
Trying to compare performance specifications across vendor websites and marketing material can also be a challenge, so we compiled a table with metrics that include scan rates, resolution, and MS/MS capabilities reported for each platform.
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Nick Riley @nmriley.bsky.social · 17/11/2023
Trent Peters-Clarke did awesome work to compile not only modern trends in instrument use (image above), but also how new instruments have impacted the balance of sensitivity and throughput in proteomics.
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