Evidence map›Paper›PMID 41663542›Full record

ArticleNature biotechnology2026

Sensitive detection of cancer antigens enabled by user-defined peptide libraries.

Kasidet Manakongtreecheep, Claudia Ctortecka, Luis O Correa-Medero, Timothy Zhu, Isabelle Lippincott, Griffin M Lawrence, Alexis Howard, Gabrielle M Hernandez, Cleo Forman, Emma C Duggan and 15 more

Abstract read
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In one paragraph

Article in Nature biotechnology, 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. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

25 authors.

Kasidet Manakongtreecheep *Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-4182-9603
Claudia Ctortecka *Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-6886-8936
Luis O Correa-MederoBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-0345-5938
Timothy ZhuBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Isabelle LippincottBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0009-0006-9034-5150
Griffin M LawrenceBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-6308-123X
Alexis HowardDana Farber Cancer Institute, Boston, MA, USA.
Gabrielle M HernandezBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Cleo FormanDana Farber Cancer Institute, Boston, MA, USA.
Emma C DugganBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Marta A WilbrinkBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0009-0005-1661-4466
Eva K VerzaniBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Alexander B AfeyanHarvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-0525-7166
Jiaxun LiDana Farber Cancer Institute, Boston, MA, USA.
Alexey I NesvizhskiiDepartment of Pathology, University of Michigan, Ann Arbor, MI, USA.ORCID http://orcid.org/0000-0002-2806-7819
Giacomo OliveiraDana Farber Cancer Institute, Boston, MA, USA.ORCID http://orcid.org/0000-0001-7435-5603
Derin B KeskinBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-8496-6181
Patrick A OttBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-4253-943X
Karl R ClauserBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-1052-9456
Matthew BakalarBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Siranush SarkizovaBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-2530-8610
Nir HacohenBroad Institute of MIT and Harvard, Cambridge, MA, USA. nhacohen@broadinstitute.org.ORCID http://orcid.org/0000-0002-2349-2656
Steven A CarrBroad Institute of MIT and Harvard, Cambridge, MA, USA. scarr@broad.mit.edu.ORCID http://orcid.org/0000-0002-7203-4299
Jennifer G AbelinBroad Institute of MIT and Harvard, Cambridge, MA, USA. jabelin@broadinstitute.org.
Catherine J WuBroad Institute of MIT and Harvard, Cambridge, MA, USA. catherine_wu@dfci.harvard.edu.ORCID http://orcid.org/0000-0002-3348-5054

Funding

Cancer Immune Monitoring and Analysis CenterU24CA224331 · NCI · DANA-FARBER CANCER INST · PI FRANK S HODI, Catherine Ju-Ying Wu · 2017 to 2026
$18.4M
ProteomicsP01CA206978 · NCI · DANA-FARBER CANCER INST · PI WU, CATHERINE JU-YING · 2016 to 2025
$17.0M
Personal tumor neoantigens for immunity against chronic lymphocytic leukemiaR01CA155010 · NCI · DANA-FARBER CANCER INST · PI Catherine Ju-Ying Wu · 2011 to 2026
$9.6M
Center of Excellence for High Throughput Proteogenomic CharacterizationU24CA270823 · NCI · BROAD INSTITUTE, INC. · PI STEVEN A CARR, MICHAEL A GILLETTE · 2022 to 2026
$5.3M
Proteogenomic Predictors of Recurrence in Non-small Cell Lung CancerU01CA271402 · NCI · WASHINGTON UNIVERSITY · PI STEVEN A CARR, MICHAEL A GILLETTE · 2022 to 2026
$5.0M
Dissecting neoepitope-specific clonal T cell populations in advanced melanoma patients vaccinated with personal neoantigen peptides partnered with local and systemic immune checkpoint InhibitionR01CA229261 · NCI · DANA-FARBER CANCER INST · PI Patrick Alexander Ott · 2018 to 2026
$3.8M
U.S. Department of Health & Human Services | National Institutes of Health (NIH) P01CA206978U.S. Department of Health & Human Services | National Institutes of Health (NIH) R01CA155010U.S. Department of Health & Human Services | National Institutes of Health (NIH) U01CA271402U.S. Department of Health & Human Services | National Institutes of Health (NIH) U24CA270823U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) R01CA229261U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) U24CA224331
6 · The paper itself

Abstract

Human leukocyte antigen (HLA)-bound tumor peptides can be routinely isolated from cancer samples and identified using mass spectrometry (MS). However, MS approaches can be stochastic or rely on spectral libraries, which are not customarily available for individual-specific peptides, thus limiting the ability to discover novel peptides. Here, we introduce Pepyrus, which generates user-defined, individual-specific or disease-specific peptide libraries in Escherichia coli to improve the sensitivity and confidence of MS peptide identification, including lowly abundant neoantigens. Using Pepyrus-generated peptide libraries paired with an HLA-specific data-independent acquisition strategy, we recover >75% of the expected sequences per single injection for libraries of >10,000 peptides and identify 0.1 fmol of spiked-in peptides in a complex background. We apply Pepyrus to create personalized libraries, facilitating identification of clinically relevant HLA peptides, including several novel peptides from cell lines derived from persons with melanoma and renal cell carcinoma. Pepyrus enables identification of rare HLA-bound peptides and provides the ability to generate large training datasets to improve spectra, retention time and ion mobility prediction tools.

Identifiers

PMID41663542

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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.