Evidence map›Paper›PMID 37012232›Full record

ArticleNature communications2023

Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues.

Jennifer G Abelin, Erik J Bergstrom, Keith D Rivera, Hannah B Taylor, Susan Klaeger, Charles Xu, Eva K Verzani, C Jackson White, Hilina B Woldemichael, Maya Virshup and 13 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.

0numbers the graph read from it
0cells of the map it votes in
42citing papers in PubMed
7.8field-weighted citation impact, top 2% of its field
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

42 citing papers in PubMed, 54 citations in OpenAlex.

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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

23 authors at 1 institution in 1 country.

Jennifer G Abelin *Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA. jabelin@broadinstitute.org.ORCID 0000-0001-5262-7241
Erik J Bergstrom *Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
Keith D RiveraBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0003-2979-9576
Hannah B TaylorBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0003-2146-8764
Susan KlaegerBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0002-0074-5163
Charles XuBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
Eva K VerzaniBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
C Jackson WhiteBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
Hilina B WoldemichaelBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
Maya VirshupBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
Meagan E OliveBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0001-8287-9474
Myranda MaynardBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
Stephanie A VartanyBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
Joseph D AllenBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0002-8951-0677
Kshiti PhulphagarBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
M Harry KaneBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0001-5677-824X
Suzanna RachimiBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
D R ManiBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0003-3914-133X
Michael A GilletteBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0001-9300-1448
Shankha SatpathyBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0002-6040-4854
Karl R ClauserBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
Namrata D UdeshiBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA. udeshi@broadinstitute.org.ORCID 0000-0001-5312-1402
Steven A CarrBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA. scarr@broad.mit.edu.ORCID 0000-0002-7203-4299
Broad Institute · US

Funding

ProteomicsP01CA206978 · NCI · DANA-FARBER CANCER INST · PI WU, CATHERINE JU-YING · 2016 to 2025
$17.0M
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
Center for comprehensive proteogenomic data analysisU24CA271075 · NCI · BROAD INSTITUTE, INC. · PI GAD A GETZ, Denkanikota R Mani · 2022 to 2026
$3.9M
NCI NIH HHS P01 CA206978NCI NIH HHS U01 CA271402NCI NIH HHS U24 CA270823NCI NIH HHS U24 CA271075
6 · The paper itself

Abstract

Serial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights into changes in protein expression, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and treatment. However, ubiquitylome and HLA peptidome data collection used to understand protein degradation and antigen presentation have not together been serialized, and instead require separate samples for parallel processing using distinct protocols. Here we present MONTE, a highly sensitive multi-omic native tissue enrichment workflow, that enables serial, deep-scale analysis of HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome, and acetylome from the same tissue sample. We demonstrate that the depth of coverage and quantitative precision of each 'ome is not compromised by serialization, and the addition of HLA immunopeptidomics enables the identification of peptides derived from cancer/testis antigens and patient specific neoantigens. We evaluate the technical feasibility of the MONTE workflow using a small cohort of patient lung adenocarcinoma tumors.

Indexed as

Lung NeoplasmsProteomeHumansMalePeptidesProteomicsWorkflowPeptidesProteome

Identifiers

PMID37012232
PMCPMC10070353
OpenAlexW4362522757

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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 Socratic graph.