Evidence map›Paper›PMID 42907640›Full record

ReviewAdvances in experimental medicine and biology2026

Developing Well-Annotated Species-Specific Protein Databases Using Comparative Proteogenomics: An Update.

Emmalyn J Dupree, Bernard S Crimmins, Thomas M Holsen, Costel C Darie

Abstract readReview
PubMed Publisher
In one paragraph

Review in Advances in experimental medicine and biology, 2026. 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

4 authors.

Emmalyn J DupreeBiochemistry & Proteomics Laboratories, Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY, 13699-5810, USA. Emmalyn.dupree@thermofisher.com.
Bernard S CrimminsDepartment of Civil and Environmental Engineering, Clarkson University, Potsdam, NY, 13699-5810, USA.
Thomas M HolsenDepartment of Civil and Environmental Engineering, Clarkson University, Potsdam, NY, 13699-5810, USA. tholsen@clarkson.edu.
Costel C DarieBiochemistry & Proteomics Laboratories, Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY, 13699-5810, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Proteomics is a mass spectrometry-based discipline that aims to analyze proteomes and their functions. Many proteomic studies require well-developed protein databases for reference. However, most proteomes are not well-annotated, aside from model organisms. Techniques like six-frame translation, ab initio gene prediction, and EST databases can aid in maximizing the amount of proteins identified in proteomics experiments, however, each of these has its downfalls. Proteogenomics is a term used to describe the union of proteomics, genomics and transcriptomics to assist in the identification of peptides which would help build better annotated proteome databases. Here, current proteomic and proteogenomic methods will be reviewed, and an example of a comparative proteomics method using lake trout liver samples will be described.

Indexed as

Databases, ProteinMolecular Sequence AnnotationProteogenomicsProteomeAnimalsProteomicsSpecies SpecificityTroutProteomeEvolutionary proteomicsFishLake troutProtein databaseProteogenomics

Identifiers

PMID42907640

What OpenQuestion holds

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Registered trials

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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.