GeenaR: A Web Tool for Reproducible MALDI-TOF Analysis.
cancer analysis
mass spectrometry
proteomics
reproducible research
web tool
Journal
Frontiers in genetics
ISSN: 1664-8021
Titre abrégé: Front Genet
Pays: Switzerland
ID NLM: 101560621
Informations de publication
Date de publication:
2021
2021
Historique:
received:
30
11
2020
accepted:
01
03
2021
entrez:
15
4
2021
pubmed:
16
4
2021
medline:
16
4
2021
Statut:
epublish
Résumé
Mass spectrometry is a widely applied technology with a strong impact in the proteomics field. MALDI-TOF is a combined technology in mass spectrometry with many applications in characterizing biological samples from different sources, such as the identification of cancer biomarkers, the detection of food frauds, the identification of doping substances in athletes' fluids, and so on. The massive quantity of data, in the form of mass spectra, are often biased and altered by different sources of noise. Therefore, extracting the most relevant features that characterize the samples is often challenging and requires combining several computational methods. Here, we present GeenaR, a novel web tool that provides a complete workflow for pre-processing, analyzing, visualizing, and comparing MALDI-TOF mass spectra. GeenaR is user-friendly, provides many different functionalities for the analysis of the mass spectra, and supports reproducible research since it produces a human-readable report that contains function parameters, results, and the code used for processing the mass spectra. First, we illustrate the features available in GeenaR. Then, we describe its internal structure. Finally, we prove its capabilities in analyzing oncological datasets by presenting two case studies related to ovarian cancer and colorectal cancer. GeenaR is available at
Identifiants
pubmed: 33854526
doi: 10.3389/fgene.2021.635814
pmc: PMC8039533
doi:
Types de publication
Journal Article
Langues
eng
Pagination
635814Informations de copyright
Copyright © 2021 Del Prete, Facchiano, Profumo, Angelini and Romano.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
Anal Chem. 2006 Jul 1;78(13):4281-90
pubmed: 16808434
Sci Rep. 2019 Aug 2;9(1):11267
pubmed: 31375721
Methods Mol Biol. 2010;604:319-31
pubmed: 20013381
Brief Bioinform. 2018 Jan 1;19(1):1-11
pubmed: 27694351
Anal Chem. 2019 Feb 5;91(3):1738-1742
pubmed: 30644722
Nucleic Acids Res. 2020 Jan 8;48(D1):D1153-D1163
pubmed: 31665479
PLoS One. 2020 Jun 29;15(6):e0234989
pubmed: 32598367
Lancet. 2002 Feb 16;359(9306):572-7
pubmed: 11867112
Nat Methods. 2015 Feb;12(2):115-21
pubmed: 25633503
Curr Opin Chem Biol. 2008 Oct;12(5):483-90
pubmed: 18718552
Nat Biotechnol. 2014 Mar;32(3):223-6
pubmed: 24727771
Diagnostics (Basel). 2020 Dec 11;10(12):
pubmed: 33322644
PLoS Med. 2005 Aug;2(8):e124
pubmed: 16060722
J Microbiol Methods. 2008 Feb;72(2):206-7
pubmed: 18166237
Int J Mol Sci. 2017 Feb 25;18(3):
pubmed: 28245601
J Biotechnol. 2017 Nov 10;261:142-148
pubmed: 28559010
Nucleic Acids Res. 2017 Jan 4;45(D1):D1100-D1106
pubmed: 27924013
Anal Chem. 2017 Sep 5;89(17):9069-9076
pubmed: 28753268
Expert Rev Proteomics. 2018 Aug;15(8):683-696
pubmed: 30058389
Proteomics. 2003 Sep;3(9):1692-8
pubmed: 12973727
Anal Bioanal Chem. 2013 Jul;405(17):5645-53
pubmed: 23539099
Curr Opin Biotechnol. 2015 Aug;34:162-70
pubmed: 25636126
J Chromatogr A. 2007 Nov 23;1172(2):135-50
pubmed: 17959187
BMC Bioinformatics. 2016 Mar 02;17 Suppl 4:61
pubmed: 26961516
Science. 2011 Dec 2;334(6060):1226-7
pubmed: 22144613
Biomark Med. 2014;8(2):269-86
pubmed: 24521024
Gigascience. 2020 Jun 1;9(6):
pubmed: 32479592
PLoS Comput Biol. 2017 Nov 3;13(11):e1005752
pubmed: 29099853
Biomed Res Int. 2016;2016:7972351
pubmed: 26977414
J Agric Food Chem. 2008 Dec 10;56(23):11071-6
pubmed: 19007297
Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450
pubmed: 30395289
Nat Protoc. 2016 Dec;11(12):2301-2319
pubmed: 27809316
Bioinformatics. 2015 Nov 15;31(22):3718-20
pubmed: 26209431
Bioinformatics. 2012 Sep 1;28(17):2270-1
pubmed: 22796955
PLoS Comput Biol. 2013 Oct;9(10):e1003285
pubmed: 24204232
Brief Bioinform. 2018 Nov 16;:
pubmed: 30452543
Adv Exp Med Biol. 2016;939:63-89
pubmed: 27807744
Int J Cancer. 2015 Nov 15;137(10):2394-402
pubmed: 25994113
J Proteomics. 2013 Jun 24;85:44-52
pubmed: 23639844
BMC Bioinformatics. 2010 Apr 29;11:219
pubmed: 20429928
Bioinformatics. 2018 Feb 1;34(3):522-523
pubmed: 29028890
Bioinformatics. 2020 May 1;36(10):3148-3155
pubmed: 32096818
Anal Chem. 2019 Aug 6;91(15):9403-9406
pubmed: 31305071
Am J Biomed Sci. 2012;4(1):85-101
pubmed: 22229059
Curr Protoc Bioinformatics. 2018 Dec;64(1):e59
pubmed: 30422396