Evidence map›Paper›PMID 35286768›Full record

ArticleProteomics2022

ProSight Annotator: Complete control and customization of protein entries in UniProt XML files.

Joseph B Greer, Bryan P Early, Kenneth R Durbin, Steven M Patrie, Paul M Thomas, Neil L Kelleher, Richard D LeDuc, Ryan T Fellers

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Proteomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Journal of the American Society for Mass Spectrometry · 2023
    Article
  3. Article
  4. Review
  5. 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

8 authors.

Joseph B GreerDepartments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.
Bryan P EarlyDepartments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.
Kenneth R DurbinDepartments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.
Steven M PatrieDepartments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.
Paul M ThomasDepartments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.
Neil L KelleherDepartments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.
Richard D LeDucDepartments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.
Ryan T FellersDepartments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.

Funding

The UIUC Neuroproteomics Center on Cell-Cell SignalingP30DA018310 · NIDA · UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN · PI Elena V Romanova · 2004 to 2026
$24.9M
TR&D 7: Cell Specific ProteomicsP41GM108569 · NIGMS · NORTHWESTERN UNIVERSITY · PI KELLEHER, NEIL L · 2015 to 2024
$13.6M
Eukaryotic Post-Translational ModificationsR01GM067193 · NIGMS · UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN · PI KELLEHER, NEIL L · 2003 to 2015
$4.0M
Defining native proteoform landscape for amyloid-beta in Alzheimers diseaseRF1AG063903 · NIA · NORTHWESTERN UNIVERSITY · PI KELLEHER, NEIL L, KLEIN, WILLIAM L · 2019 to 2019
$2.9M
Algorithms for Glyco-Proteoform DetectionR01GM115739 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI PATRIE, STEVEN MATTHEW · 2016 to 2020
$1.9M
NIA NIH HHS RF1 AG063903NIDA NIH HHS P30 DA018310NIGMS NIH HHS GM067193NIGMS NIH HHS P41 GM108569NIGMS NIH HHS R01 GM067193NIGMS NIH HHS R01 GM115739
6 · The paper itself

Abstract

The effectiveness of any proteomics database search depends on the theoretical candidate information contained in the protein database. Unfortunately, candidate entries from protein databases such as UniProt rarely contain all the post-translational modifications (PTMs), disulfide bonds, or endogenous cleavages of interest to researchers. These omissions can limit discovery of novel and biologically important proteoforms. Conversely, searching for a specific proteoform becomes a computationally difficult task for heavily modified proteins. Both situations require updates to the database through user-annotated entries. Unfortunately, manually creating properly formatted UniProt Extensible Markup Language (XML) files is tedious and prone to errors. ProSight Annotator solves these issues by providing a graphical interface for adding user-defined features to UniProt-formatted XML files for better informed proteoform searches. It can be downloaded from http://prosightannotator.northwestern.edu.

Indexed as

LanguageProteinsDatabases, ProteinProtein Processing, Post-TranslationalProteomicsSoftwareProteinsbottom-up proteomicspost-translational modificationproteoformsproteomics softwaretop-down proteomicsUniProt

Identifiers

PMID35286768
PMCPMC9188994

What OpenQuestion holds

Textmetadata
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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.