Evidence map›Paper›PMID 38478054›Full record

ArticleJournal of proteome research2024

Fit for Purpose Approach To Evaluate Detection of Amino Acid Substitutions in Shotgun Proteomics.

Taylor J Lundgren, Patricia L Clark, Matthew M Champion

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

Article in Journal of proteome research, 2024. 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
0.5field-weighted citation impact, top 44% 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

1 citing paper in PubMed, 2 citations in OpenAlex.

  1. 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

3 authors at 1 institution in 1 country.

Taylor J LundgrenDepartment of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.
Patricia L ClarkDepartment of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.ORCID 0000-0001-5462-8248
Matthew M ChampionDepartment of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.ORCID 0000-0001-5927-5277
University of Notre Dame · US

Funding

Decoding the regulation of protein folding by synonymous codon usageDP1GM146256 · NIGMS · UNIVERSITY OF NOTRE DAME · PI CLARK, PATRICIA LOUISE · 2021 to 2025
$5.5M
Chemistry-Biochemistry-Biology Training Program at Notre DameT32GM075762 · NIGMS · UNIVERSITY OF NOTRE DAME · PI CHANG, MAYLAND F, MOBASHERY, SHAHRIAR · 2007 to 2021
$3.7M
Systematic Discovery and Analysis of Small Proteins and Small ORFs in MycobacteriaR01GM139277 · NIGMS · WADSWORTH CENTER · PI DERBYSHIRE, KEITH M, GRAY, TODD · 2020 to 2023
$2.2M
NIGMS NIH HHS DP1 GM146256NIGMS NIH HHS R01 GM139277NIGMS NIH HHS T32 GM075762
6 · The paper itself

Abstract

Amino acid substitutions (AASs) alter proteins from their genome-expected sequences. Accumulation of substitutions in proteins underlies numerous diseases and antibiotic mechanisms. Accurate global detection of AASs and their frequencies is crucial for understanding these mechanisms. Shotgun proteomics provides an untargeted method for measuring AASs but introduces biases when extrapolating from the genome to identify AASs. To characterize these biases, we created a "ground-truth" approach using the similarities between

Indexed as

Escherichia coliProteomicsAmino Acid SubstitutionPeptidesProteinsPeptidesProteinsamino acid substitutionbioinformaticsbottom-up proteomicsground truthspectral library

Identifiers

PMID38478054
PMCPMC11003417
OpenAlexW4392740297

What OpenQuestion 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 OpenQuestion graph.