Evidence map›Paper›PMID 30737169›Full record

ArticleRedox biology2019

oxSWATH: An integrative method for a comprehensive redox-centered analysis combined with a generic differential proteomics screening.

Sandra I Anjo, Matilde N Melo, Liliana R Loureiro, Lúcia Sabala, Pedro Castanheira, Mário Grãos, Bruno Manadas

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Redox biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing 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

11 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Review
  5. Article
  6. Review
  7. Review
  8. Review
  9. Review
  10. Review
  11. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Sandra I AnjoCenter for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal; Faculty of Medicine, University of Coimbra, Coimbra, Portugal. Electronic address: sandra.anjo@cnc.uc.pt.
Matilde N MeloCenter for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.
Liliana R LoureiroCenter for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Department of Chemistry, University of Aveiro, Aveiro, Portugal.
Lúcia SabalaCenter for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Department of Chemistry, University of Aveiro, Aveiro, Portugal.
Pedro CastanheiraBiocant, Technology Transfer Association, Cantanhede, Portugal.
Mário GrãosCenter for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Biocant, Technology Transfer Association, Cantanhede, Portugal.
Bruno ManadasCenter for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Most of the redox proteomics strategies are focused on the identification and relative quantification of cysteine oxidation without considering the variation in the total levels of the proteins. However, protein synthesis and protein degradation also belong to the regulatory mechanisms of the cells, being therefore important to consider the changes in total protein levels in PTMs-focused analyses, such as cysteine redox characterization. Therefore, a novel integrative approach combining the SWATH-MS method with differential alkylation using a combination of commonly available alkylating reagents (oxSWATH) is presented, by which it is possible to integrate the information regarding relative cysteine oxidation with the analysis of the total protein levels in a cost-effective high-throughput approach. The proposed method was tested using a redox-regulated protein and further applied to a comparative analysis of secretomes obtained from cells cultured under control or oxidative stress conditions to strengthen the importance of considering the overall proteome changes. Using the OxSWATH method it was possible to determine both the relative proportion of reduced and reversible oxidized oxoforms, as well as the total levels of each oxoform by taking into consideration the total levels of the protein. Therefore, using OxSWATH the comparative analyses can be performed at two different levels by considering the relative proportion or the total levels at both peptide and protein level. Moreover, since samples are acquired in SWATH-MS mode, besides the redox centered analysis, a generic differential protein expression analysis can also be performed, allowing a truly comprehensive evaluation of proteomics changes upon the oxidative stimulus. Data are available via ProteomeXchange and SWATHAtlas with the identifiers PXD006802, PXD006802, and PASS01210.

Identifiers

PMID30737169
PMCPMC6435957

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.