Evidence map›Paper›PMID 36595954›Full record

ArticleSTAR protocols2022

HLA-I immunopeptidome profiling of human cells infected with high-containment enveloped viruses.

Shira Weingarten-Gabbay, Leah R Pearlman, Da-Yuan Chen, Susan Klaeger, Hannah B Taylor, Nicole L Welch, Derin B Keskin, Steven A Carr, Jennifer G Abelin, Mohsan Saeed and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. The diverse functions of viral microproteins.bioRxiv : the preprint server for biology · 2026
    Article
  2. Article
  3. Article
  4. Article
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

11 authors.

Shira Weingarten-GabbayBroad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA. Electronic address: shirawg@broadinstitute.org.
Leah R PearlmanBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Da-Yuan ChenDepartment of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
Susan KlaegerBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Hannah B TaylorBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Nicole L WelchBroad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Virology, Harvard Medical School, Boston, MA, USA.
Derin B KeskinBroad Institute of MIT and Harvard, Cambridge, MA, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.
Steven A CarrBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Jennifer G AbelinBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Mohsan SaeedDepartment of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
Pardis C SabetiBroad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA; Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.

Funding

Viral Genomics: evolution, spread, and host interactionsU19AI110818 · NIAID · BROAD INSTITUTE, INC. · PI NEAFSEY, DANIEL E · 2014 to 2024
$66.5M
Center of Excellence for High Throughput Proteogenomic CharacterizationU24CA210986 · NCI · BROAD INSTITUTE, INC. · PI CARR, STEVEN A, GILLETTE, MICHAEL A · 2016 to 2020
$6.4M
Center of Excellence for High Throughput Proteogenomic CharacterizationU24CA270823 · NCI · BROAD INSTITUTE, INC. · PI STEVEN A CARR, MICHAEL A GILLETTE · 2022 to 2026
$5.3M
Integrated high throughput proteogenomic data analysis center for CPTACU24CA210979 · NCI · BROAD INSTITUTE, INC. · PI BIRGER, CHET, GETZ, GAD A · 2016 to 2020
$4.4M
Center for comprehensive proteogenomic data analysisU24CA271075 · NCI · BROAD INSTITUTE, INC. · PI GAD A GETZ, Denkanikota R Mani · 2022 to 2026
$3.9M
Systematic identification of minor histocompatibility antigens to address GVHDR01HL157174 · NHLBI · DANA-FARBER CANCER INST · PI HO, VINCENT TRIEN-VINH, KESKIN, DERIN B · 2022 to 2025
$3.0M
NCI NIH HHS U24 CA210979NCI NIH HHS U24 CA210986NCI NIH HHS U24 CA270823NCI NIH HHS U24 CA271075NHLBI NIH HHS R01 HL157174NIAID NIH HHS U19 AI110818
6 · The paper itself

Abstract

Immunopeptidome profiling of infected cells is a powerful technique for detecting viral peptides that are naturally processed and loaded onto class I human leukocyte antigens (HLAs-I). Here, we provide a protocol for preparing samples for immunopeptidome profiling that can inactivate enveloped viruses while still preserving the integrity of the HLA-I complex. We detail steps for lysate preparation of infected cells followed by HLA-I immunoprecipitation and virus inactivation. We further describe peptide purification for mass spectrometry outside a high-containment facility. For complete details on the use and execution of this protocol, please refer to Weingarten-Gabbay et al. (2021).

Indexed as

Histocompatibility Antigens Class IVirusesHumansMass SpectrometryPeptidesHistocompatibility Antigens Class IPeptidesImmunologyMass SpectrometryMicrobiology

Identifiers

PMID36595954
PMCPMC9731565

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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 OpenQuestion graph.