Evidence map›Paper›PMID 39493671›Full record

ArticleISME communications2024

NovoLign: metaproteomics by sequence alignment.

Hugo B C Kleikamp, Ramon van der Zwaan, Ramon van Valderen, Jitske M van Ede, Mario Pronk, Pim Schaasberg, Maximilienne T Allaart, Mark C M van Loosdrecht, Martin Pabst

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In one paragraph

Article in ISME communications, 2024. 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
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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

9 authors.

Hugo B C KleikampDepartment of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629HZ, The Netherlands.
Ramon van der ZwaanDepartment of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629HZ, The Netherlands.
Ramon van ValderenDepartment of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629HZ, The Netherlands.
Jitske M van EdeDepartment of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629HZ, The Netherlands.
Mario PronkDepartment of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629HZ, The Netherlands.
Pim SchaasbergDepartment of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629HZ, The Netherlands.
Maximilienne T AllaartDepartment of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629HZ, The Netherlands.
Mark C M van LoosdrechtDepartment of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629HZ, The Netherlands.
Martin PabstDepartment of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629HZ, The Netherlands.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome sequencing experiments. However, creating these databases is complex, time-consuming, and prone to errors, potentially biasing experimental outcomes and conclusions. This asks for alternative approaches that can provide rapid and orthogonal insights into metaproteomics data. Here, we present NovoLign, a

Indexed as

de novo sequencingmetaproteomicsmicrobial communitiessequence alignment

Identifiers

PMID39493671
PMCPMC11530927

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.