Evidence map›Paper›PMID 29977167›Full record

ArticleJournal of biomolecular techniques : JBT2018

ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data.

Joon-Yong Lee, Hyungwon Choi, Christopher M Colangelo, Darryl Davis, Michael R Hoopmann, Lukas Käll, Henry Lam, Samuel H Payne, Yasset Perez-Riverol, Matthew The and 3 more

Abstract read
In one paragraph

Article in Journal of biomolecular techniques : JBT, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
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

13 authors.

Joon-Yong LeePacific Northwest National Laboratory, Richland, Washington 99352, USA.
Hyungwon ChoiNational University of Singapore, 117547 Singapore, Singapore.
Christopher M ColangeloAgilent Technologies, 121 Hartwell Ave., Lexington, MA 02421.
Darryl DavisJanssen Research and Development, Spring House, Pennsylvania 19087, USA.
Michael R HoopmannInstitute for Systems Biology, Seattle, Washington 98109, USA.
Lukas KällScience for Life Laboratory, KTH - Royal Institute of Technology, 171 65 Solna, Sweden.
Henry LamDepartment of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
Samuel H PaynePacific Northwest National Laboratory, Richland, Washington 99352, USA.
Yasset Perez-RiverolEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
Matthew TheScience for Life Laboratory, KTH - Royal Institute of Technology, 171 65 Solna, Sweden.
Ryan WilsonPacific Northwest National Laboratory, Richland, Washington 99352, USA.
Susan T WeintraubDepartment of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, Texas 78229, USA; and.
Magnus PalmbladCenter for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.

Funding

Quantitative Systems BiologyP50GM076547 · NIGMS · INSTITUTE FOR SYSTEMS BIOLOGY · PI BALIGA, NITIN S · 2006 to 2016
$30.6M
COPD Susceptibility, Heterogeneity, and Progression: Proteomics and GeneticsR01HL133135 · NHLBI · BRIGHAM AND WOMEN'S HOSPITAL · PI MORITZ, ROBERT L, SILVERMAN, EDWIN K · 2017 to 2025
$7.2M
Shortening the development cycle time of Trans Proteomic Pipeline tools with high performance computingR01GM087221 · NIGMS · INSTITUTE FOR SYSTEMS BIOLOGY · PI DEUTSCH, ERIC, MORITZ, ROBERT L · 2010 to 2021
$6.0M
NHLBI NIH HHS R01 HL133135NIGMS NIH HHS P50 GM076547NIGMS NIH HHS R01 GM087221
6 · The paper itself

Abstract

This report presents the results from the 2016 Association of Biomolecular Resource Facilities Proteome Informatics Research Group (iPRG) study on proteoform inference and false discovery rate (FDR) estimation from bottom-up proteomics data. For this study, 3 replicate Q Exactive Orbitrap liquid chromatography-tandom mass spectrometry datasets were generated from each of 4

Indexed as

Databases, FactualChromatography, LiquidComputational BiologyEscherichia coliHumansProteomeProteomicsSoftwareTandem Mass SpectrometryProteomebest practicecommunity studyfalse discovery rateinference

Identifiers

PMID29977167
PMCPMC6011817

What OpenQuestion holds

Textmetadata
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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.