Evidence map›Paper›PMID 31768060›Full record

ArticleNature methods2020

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput.

Vadim Demichev, Christoph B Messner, Spyros I Vernardis, Kathryn S Lilley, Markus Ralser

Abstract read
In one paragraph

Article in Nature methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,954 papers.

0numbers the graph read from it
0cells of the map it votes in
1,954citing 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

1,954 citing papers in PubMed.

  1. Preprocessing Large-Scale Proteomics Data.Methods in molecular biology (Clifton, N.J.) · 2027
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  3. Mass Spectrometry-Based Proteomics of Intestinal Organoids.Methods in molecular biology (Clifton, N.J.) · 2027
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  8. GutGut microbes · 2026
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1,894 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

5 authors.

Vadim DemichevDepartment of Biochemistry and The Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0002-2424-9412
Christoph B MessnerThe Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK.
Spyros I VernardisThe Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK.
Kathryn S LilleyDepartment of Biochemistry and The Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0003-0594-6543
Markus RalserThe Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK. markus.ralser@crick.ac.uk.ORCID http://orcid.org/0000-0001-9535-7413

Funding

Biotechnology and Biological Sciences Research Council BB/N015215/1Biotechnology and Biological Sciences Research Council BB/N015282/1Medical Research Council MC_PC_17179Medical Research Council MC_UP_1202/8Wellcome Trust 200829Wellcome Trust FC001134
6 · The paper itself

Abstract

We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments. DIA-NN improves the identification and quantification performance in conventional DIA proteomic applications, and is particularly beneficial for high-throughput applications, as it is fast and enables deep and confident proteome coverage when used in combination with fast chromatographic methods.

Indexed as

Neural Networks, ComputerSoftwareHeLa CellsHigh-Throughput Screening AssaysHumansMass SpectrometryProteomeProteomicsSpecies SpecificityZea maysProteome

Identifiers

PMID31768060
PMCPMC6949130

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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.