Evidence map›Paper›PMID 31573204›Full record

ReviewJournal of proteome research2019

Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data.

Vera Ignjatovic, Philipp E Geyer, Krishnan K Palaniappan, Jessica E Chaaban, Gilbert S Omenn, Mark S Baker, Eric W Deutsch, Jochen M Schwenk

Abstract readReview
In one paragraph

Review in Journal of proteome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 126 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
126citing papers in PubMed, 1 pooled it
–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

126 citing papers in PubMed, 1 synthesis or guideline pooled it.

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66 more citing papers are in PubMed but not listed here.

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.

Vera IgnjatovicHaematology Research , Murdoch Children's Research Institute , Parkville , VIC 3052 , Australia.
Philipp E GeyerNNF Center for Protein Research, Faculty of Health Sciences , University of Copenhagen , 2200 Copenhagen , Denmark.
Krishnan K PalaniappanFreenome , 259 East Grand Avenue , South San Francisco , California 94080 , United States.ORCID 0000-0003-0203-9016
Jessica E ChaabanHaematology Research , Murdoch Children's Research Institute , Parkville , VIC 3052 , Australia.
Gilbert S OmennDepartments of Computational Medicine & Bioinformatics, Human Genetics, and Internal Medicine and School of Public Health , University of Michigan , 100 Washtenaw Avenue , Ann Arbor , Michigan 48109-2218 , United States.ORCID 0000-0002-8976-6074
Mark S BakerDepartment of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , 75 Talavera Road , North Ryde , NSW 2109 , Australia.ORCID 0000-0001-5858-4035
Eric W DeutschInstitute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States.ORCID 0000-0001-8732-0928
Jochen M SchwenkAffinity Proteomics, SciLifeLab , KTH Royal Institute of Technology , 171 65 Stockholm , Sweden.ORCID 0000-0001-8141-8449

Funding

Systems BiologyU19AG023122 · NIA · TRANSLATIONAL GENOMICS RESEARCH INST · PI Thomas Girke, NICHOLAS Joseph SCHORK · 2004 to 2026
$102.6M
Strategic Vision & Impact on Environmental HealthP30ES017885 · NIEHS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Dana Dolinoy · 2011 to 2026
$21.3M
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
University of Michigan Proteogenomics Data Analysis CenterU24CA210967 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI CHINNAIYAN, ARUL M, DHANASEKARAN, SARAVANA M · 2016 to 2020
$4.1M
Advancing data and metadata standards for proteomics mass spectraR24GM127667 · NIGMS · INSTITUTE FOR SYSTEMS BIOLOGY · PI DEUTSCH, ERIC · 2017 to 2019
$1.2M
NCI NIH HHS U24 CA210967NIA NIH HHS U19 AG023122NIEHS NIH HHS P30 ES017885NIGMS NIH HHS R01 GM087221NIGMS NIH HHS R24 GM127667
6 · The paper itself

Abstract

The proteomic analysis of human blood and blood-derived products (e.g., plasma) offers an attractive avenue to translate research progress from the laboratory into the clinic. However, due to its unique protein composition, performing proteomics assays with plasma is challenging. Plasma proteomics has regained interest due to recent technological advances, but challenges imposed by both complications inherent to studying human biology (e.g., interindividual variability) and analysis of biospecimens (e.g., sample variability), as well as technological limitations remain. As part of the Human Proteome Project (HPP), the Human Plasma Proteome Project (HPPP) brings together key aspects of the plasma proteomics pipeline. Here, we provide considerations and recommendations concerning study design, plasma collection, quality metrics, plasma processing workflows, mass spectrometry (MS) data acquisition, data processing, and bioinformatic analysis. With exciting opportunities in studying human health and disease though this plasma proteomics pipeline, a more informed analysis of human plasma will accelerate interest while enhancing possibilities for the incorporation of proteomics-scaled assays into clinical practice.

Indexed as

Blood ProteinsBlood Specimen CollectionComputational BiologyHumansMass SpectrometryProteomicsQuality ControlWorkflowBlood Proteinsbioinformatic analysisblooddata acquisitiondata processingHuman Plasma Proteome Project (HPPP)Human Proteome Project (HPP)mass spectrometry (MS)plasmaplasma processing workflowsquality metricssample collectionserumstudy design

Identifiers

PMID31573204
PMCPMC6898750

What OpenQuestion holds

Textmetadata
LicenceTDM
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.