Evidence map›Paper›PMID 38915658›Full record

ArticlebioRxiv : the preprint server for biology2025

Jordy Bollon, Michael R Shortreed, Ben T Jordan, Rachel Miller, Erin Jeffery, Andrea Cavalli, Lloyd M Smith, Colin Dewey, Gloria M Sheynkman, Simone Tiberi

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Jordy BollonComputational and Chemical Biology, Italian Institute of Technology, CMPVdA, Aosta, Italy.
Michael R ShortreedDepartment of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
Ben T JordanFrederick National Laboratory for Cancer Research, Frederick, MD, USA.
Rachel MillerDepartment of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
Erin JefferyDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
Andrea CavalliComputational and Chemical Biology, Italian Institute of Technology, CMPVdA, Aosta, Italy.
Lloyd M SmithDepartment of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
Colin DeweyDepartment of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA.
Gloria M SheynkmanDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
Simone TiberiDepartment of Statistical Sciences, University of Bologna, Bologna, Italy.ORCID 0000-0002-3054-9964

Funding

Revealing Proteoforms: The Primary Effectors of Biological FunctionR35GM126914 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI Lloyd M Smith · 2018 to 2026
$6.2M
Enhanced Sensitivity and Quantitative Precision for Single Cell ProteomicsR01GM147653 · NIGMS · BRIGHAM YOUNG UNIVERSITY · PI PAYNE, SAMUEL H, SHORTREED, MICHAEL R · 2022 to 2025
$1.6M
NIGMS NIH HHS R01 GM147653NIGMS NIH HHS R35 GM126914
6 · The paper itself

Abstract

Motivation: Studying protein isoforms is an essential step in biomedical research; at present, the main approach for analyzing proteins is via bottom-up mass spectrometry proteomics, which return peptide identifications, that are indirectly used to infer the presence of protein isoforms. However, the detection and quantification processes are noisy; in particular, peptides may be erroneously detected, and most peptides, known as shared peptides, are associated to multiple protein isoforms. As a consequence, studying individual protein isoforms is challenging, and inferred protein results are often abstracted to the gene-level or to groups of protein isoforms. Results: Here, we introduce Availability and implementation:

Identifiers

PMID38915658
PMCPMC11195044

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.