Evidence map›Paper›PMID 29790936›Full record

ArticleBioinformatics (Oxford, England)2018

SimExTargId: a comprehensive package for real-time LC-MS data acquisition and analysis.

William M B Edmands, Josie Hayes, Stephen M Rappaport

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

Article in Bioinformatics (Oxford, England), 2018. 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
0.3field-weighted citation impact, top 43% 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, 4 citations in OpenAlex.

  1. 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

3 authors at 1 institution in 1 country.

William M B EdmandsProgram in Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.
Josie HayesProgram in Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.
Stephen M RappaportProgram in Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.
Berkeley Public Health Division · US

Funding

Training CoreP42ES004705 · NIEHS · UNIVERSITY OF CALIFORNIA BERKELEY · PI SEDLAK, DAVID L. · 1987 to 2025
$74.6M
Targeted Research Training CoreT42OH008429 · OH · UNIVERSITY OF CALIFORNIA BERKELEY · PI HARRIS ADAMSON, CARISA · 2005 to 2024
$30.0M
Project 3 - Prenatal Exposures, Constitutive Genetics, DNA Methylation & Childhood LeukemiaP50ES018172 · NIEHS · UNIVERSITY OF CALIFORNIA BERKELEY · PI METAYER, CATHERINE · 2015 to 2019
$3.8M
Project 3: Prenatal Exposure, DNA Methylation & Childhood LeukemiaP01ES018172 · NIEHS · UNIVERSITY OF CALIFORNIA BERKELEY · PI METAYER, CATHERINE · 2009 to 2013
$3.7M
NIEHS NIH HHS P01 ES018172NIEHS NIH HHS P42 ES004705NIEHS NIH HHS P50 ES018172NIOSH CDC HHS T42 OH008429
6 · The paper itself

Abstract

Summary: Liquid chromatography mass spectrometry (LC-MS) is the favored method for untargeted metabolomic analysis of small molecules in biofluids. Here we present SimExTargId, an open-source R package for autonomous analysis of metabolomic data and real-time observation of experimental runs. This simultaneous, fully automated and multi-threaded (optional) package is a wrapper for vendor-independent format conversion (ProteoWizard), xcms- and CAMERA- based peak-picking, MetMSLine-based pre-processing and covariate-based statistical analysis. Users are notified of detrimental instrument drift or errors by email. Also included are two shiny applications, targetId for real-time MS2 target identification, and peakMonitor to monitor targeted metabolites. Availability and implementation: SimExTargId is publicly available under GNU LGPL v3.0 license at https://github.com/JosieLHayes/simExTargId, which includes a vignette with example data. SimExTargId should be installed on a dedicated data-processing workstation or server that is networked to the LC-MS platform to facilitate MS1 profiling of metabolomic data. Supplementary information: Supplementary data are available at Bioinformatics online.

Indexed as

SoftwareChromatography, LiquidMetabolomicsTandem Mass SpectrometryTime Factors

Identifiers

PMID29790936
PMCPMC6184452
OpenAlexW2804508533

What OpenQuestion holds

Textmetadata
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.