Evidence map›Paper›PMID 39661499›Full record

ArticleJournal of proteome research2025

Intact Mass Proteomics Using a Proteoform Atlas.

John G Pavek, Isabella T Whitworth, Lisa Nakayama, Mark Scalf, Brian L Frey, Lloyd M Smith

Abstract read
In one paragraph

Article in Journal of proteome research, 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

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

6 authors.

John G PavekDepartment of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wisconsin 53706, United States.ORCID 0009-0002-6435-1486
Isabella T WhitworthDepartment of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wisconsin 53706, United States.ORCID 0000-0001-9753-5666
Lisa NakayamaDepartment of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wisconsin 53706, United States.ORCID 0009-0009-4958-8793
Mark ScalfDepartment of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wisconsin 53706, United States.
Brian L FreyDepartment of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wisconsin 53706, United States.ORCID 0000-0002-0397-7269
Lloyd M SmithDepartment of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wisconsin 53706, United States.

Funding

Revealing Proteoforms: The Primary Effectors of Biological FunctionR35GM126914 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI Lloyd M Smith · 2018 to 2026
$6.2M
NIGMS NIH HHS R35 GM126914
6 · The paper itself

Abstract

Top-down proteomics, the characterization of intact proteoforms by tandem mass spectrometry, is the principal method for proteoform characterization in complex samples. Top-down proteomics relies on precursor isolation and subsequent gas-phase fragmentation to make proteoform identifications. While this strategy can produce highly detailed molecular information, the reliance on time-intensive tandem MS limits the speed with which proteoforms can be identified. We suggest that once proteoforms have been identified by top-down analysis in a system of interest, and archived in a system-specific Proteoform Atlas, subsequent analyses in that system can utilize the Atlas information to enable simpler and faster MS1-only identifications. We explore this idea here, using the

Indexed as

Escherichia coliEscherichia coli ProteinsProteomicsRibosomesTandem Mass SpectrometryProteomeRibosomal ProteinsEscherichia coli ProteinsProteomeRibosomal Proteinsatlasefficiencyintact-massMS1proteoformproteoformstop-down

Identifiers

PMID39661499
PMCPMC12045104

What OpenQuestion holds

Textmetadata
LicenceTDM
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.