Evidence map›Paper›PMID 42649221›Full record

ArticleNature communications2026

Next-generation multiplexed targeted proteomics quantifies post-translational modifications in disease and compound-protein interactions with high throughput.

Steven R Shuken, Geordon A Frere, Charlotte R Beard, Christopher D McGann, Jesse D Canterbury, Nathan R Zuniga, Brandon M Gassaway, Shane L Dawson, Kean Hean Ooi, João A Paulo and 3 more

Abstract read
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Steven R ShukenDepartment of Cell Biology, Harvard Medical School, Boston, MA, USA.ORCID 0000-0002-2782-2165
Geordon A FrereDepartment of Cell Biology, Harvard Medical School, Boston, MA, USA.
Charlotte R BeardMental Illness Research Education and Clinical Center (MIRECC), Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
Christopher D McGannDepartment of Cell Biology, Harvard Medical School, Boston, MA, USA.
Jesse D CanterburyThermo Fisher Scientific, San Jose, CA, USA.
Nathan R ZunigaDepartment of Cell Biology, Harvard Medical School, Boston, MA, USA.
Brandon M GassawayDepartment of Cell Biology, Harvard Medical School, Boston, MA, USA.ORCID 0000-0002-6102-2356
Shane L DawsonDepartment of Cell Biology, Harvard Medical School, Boston, MA, USA.
Kean Hean OoiDepartment of Cell Biology, Harvard Medical School, Boston, MA, USA.
João A PauloDepartment of Cell Biology, Harvard Medical School, Boston, MA, USA.ORCID 0000-0002-4291-413X
M Windy McNerneyMental Illness Research Education and Clinical Center (MIRECC), Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
Steven P GygiDepartment of Cell Biology, Harvard Medical School, Boston, MA, USA. steven_gygi@hms.harvard.edu.ORCID 0000-0001-7626-0034
Qing YuDepartment of Cell Biology, Harvard Medical School, Boston, MA, USA. qing.yu@umassmed.edu.ORCID 0000-0003-0468-5353

Funding

Advancing Multiplexed Isobaric Tag-based Strategies for Proteome ProfilingR01GM132129 · NIGMS · HARVARD MEDICAL SCHOOL · PI PAULO, JOAO A · 2019 to 2023
$1.7M
New Proteomics Approaches to Study the Full Human Kinome, Inhibitor Resistance, and Kinase DegradersK22CA282268 · NCI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI Qing Yu · 2024 to 2026
$636k
Validation and Kinetic Characterization of Blood-Cerebrospinal Fluid Barrier-Traversing Proteins in Aging With Library-Free Multiplexed Targeted ProteomicsK99AG088297 · NIA · HARVARD MEDICAL SCHOOL · PI SHUKEN, STEVEN ROBERT · 2024 to 2025
$250k
NCI NIH HHS K22 CA282268NIA NIH HHS K99 AG088297NIGMS NIH HHS R01 GM132129NIH HHS GM67945
6 · The paper itself

Abstract

The GoDig platform enables sensitive, multiplexed targeted pathway proteomics without manual scheduling or synthetic standards. Here we present GoDig 2.0, which increases sample multiplexing to 35-fold, improves time efficiency and reduces scan delays for higher success rates, and allows flexible spectral and elution library generation from different mass spectrometry data types. GoDig 2.0 measures 2.4× more targets than GoDig 1.0, quantifying >99% of 800 peptides in a single run. We compile a library of 23,989 human phosphorylation sites from a phosphoproteomic dataset and use it to profile kinase signaling differences across cell lines. In human brain tissue, we establish a hyperphosphorylated tau assay including pTau127, revealing potential biomarkers for Alzheimer's disease. We also quantify diglycyl-lysine peptides to assess polyubiquitin branching. Finally, we build a library of 20,946 reactive cysteines and profile covalent compound-protein interactions spanning diverse pathways. GoDig 2.0 enables high-throughput analyses of site-specific protein modifications across many biological contexts.

Indexed as

Alzheimer DiseaseProtein Processing, Post-TranslationalProteomicsBrainHigh-Throughput Screening AssaysHumansMass SpectrometryPhosphorylationtau Proteinstau Proteins

Identifiers

PMID42649221
PMCPMC13518854

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.