Data sharing in PredRet for accurate prediction of retention time: Application to plant food bioactive compounds
Dorrain Yanwen Low
(1)
,
Pierre Micheau
(1)
,
Ville Mikael Koistinen
(2, 3)
,
Kati Hanhineva
(4, 3)
,
László Abrankó
(5)
,
Ana Rodriguez-Mateos
(6)
,
Andreia Bento da Silva
(7, 8)
,
Christof van Poucke
(9)
,
Conceição Almeida
(7)
,
Cristina Andres-Lacueva
(10, 11)
,
Dilip Rai
(12)
,
Esra Capanoglu
(13)
,
Francisco Tomás Barberán
(14, 15)
,
Fulvio Mattivi
(16, 17)
,
Gesine Schmidt
(18)
,
Gözde Gürdeniz
(19)
,
Kateřina Valentová
(20)
,
Letizia Bresciani
(21)
,
Lucie Petrásková
(20)
,
Lars Ove Dragsted
(22, 19)
,
Mark Philo
(23)
,
Marynka Ulaszewska
(24)
,
Pedro Mena
(25)
,
Raúl González-Domínguez
(10, 11)
,
Rocío Garcia-Villalba
(14)
,
Senem Kamiloglu
(13)
,
Sonia de Pascual-Teresa
(26)
,
Stéphanie Durand
(27, 1)
,
Wieslaw Wiczkowski
(28)
,
Maria Rosário Bronze
(7)
,
Jan Stanstrup
(19)
,
Claudine Manach
(1)
1
UNH -
Unité de Nutrition Humaine
2 Institute of Public Health and Clinical Nutrition
3 University of Turku
4 Institute of Public Health and Clinical Nutrition
5 Szent István University
6 King‘s College London
7 NOVA - Universidade Nova de Lisboa = NOVA University Lisbon
8 ISCTE - University Institute of Lisbon
9 ILVO - Research Institute for Agricultural, Fisheries and Food
10 University of Barcelona
11 CIBER de Fragilidad y Envejecimiento Saludable
12 Teagasc - Teagasc Ashtown Food Research Centre
13 ITÜ - Istanbul Technical University
14 CEBAS - CSIC - Centro de Edafologia y Biologia aplicada del Segura
15 TU - Taif University
16 Fdn Edmund Mach, IASMA Research and Innovation Centre
17 UNITN - Università degli Studi di Trento = University of Trento
18 NOFIMA - Norwegian Institute of Food,Fisheries and Aquaculture Research
19 ITU - IT University of Copenhagen
20 MBU / CAS - Institute of Microbiology of the Czech Academy of Sciences [Prague, Czech Republic]
21 UNIPR - Università degli studi di Parma = University of Parma
22 Department of Nutrition, Exercise and Sports [Copenhagen]
23 QIB - Quadram Institute Bioscience [Norwich, U.K.]
24 FEM - Fondazione Edmund Mach - Edmund Mach Foundation [Italie]
25 Department of Food & Drugs
26 ICTAN-CSIC - Institute of Food Science, Technology and Nutrition
27 PFEM - Plateforme Exploration du Métabolisme
28 Institute of Animal Reproduction and Food Research of Polish Academy of Sciences
2 Institute of Public Health and Clinical Nutrition
3 University of Turku
4 Institute of Public Health and Clinical Nutrition
5 Szent István University
6 King‘s College London
7 NOVA - Universidade Nova de Lisboa = NOVA University Lisbon
8 ISCTE - University Institute of Lisbon
9 ILVO - Research Institute for Agricultural, Fisheries and Food
10 University of Barcelona
11 CIBER de Fragilidad y Envejecimiento Saludable
12 Teagasc - Teagasc Ashtown Food Research Centre
13 ITÜ - Istanbul Technical University
14 CEBAS - CSIC - Centro de Edafologia y Biologia aplicada del Segura
15 TU - Taif University
16 Fdn Edmund Mach, IASMA Research and Innovation Centre
17 UNITN - Università degli Studi di Trento = University of Trento
18 NOFIMA - Norwegian Institute of Food,Fisheries and Aquaculture Research
19 ITU - IT University of Copenhagen
20 MBU / CAS - Institute of Microbiology of the Czech Academy of Sciences [Prague, Czech Republic]
21 UNIPR - Università degli studi di Parma = University of Parma
22 Department of Nutrition, Exercise and Sports [Copenhagen]
23 QIB - Quadram Institute Bioscience [Norwich, U.K.]
24 FEM - Fondazione Edmund Mach - Edmund Mach Foundation [Italie]
25 Department of Food & Drugs
26 ICTAN-CSIC - Institute of Food Science, Technology and Nutrition
27 PFEM - Plateforme Exploration du Métabolisme
28 Institute of Animal Reproduction and Food Research of Polish Academy of Sciences
Pedro Mena
- Fonction : Auteur
- PersonId : 784054
- ORCID : 0000-0003-2150-2977
Stéphanie Durand
- Fonction : Auteur
- PersonId : 736394
- IdHAL : stephanie-durand2
- ORCID : 0000-0002-9250-5537
- IdRef : 118436511
Claudine Manach
- Fonction : Auteur
- PersonId : 736225
- IdHAL : claudine-manach
- ORCID : 0000-0003-1094-3363
- IdRef : 230917623
Résumé
Prediction of retention times (RTs) is increasingly considered in untargeted metabolomics to complement MS/MS matching for annotation of unidentified peaks. We tested the performance of PredRet (http://predret.org/) to predict RTs for plant food bioactive metabolites in a data sharing initiative containing entry sets of 29–103 compounds (totalling 467 compounds, >30 families) across 24 chromatographic systems (CSs). Between 27 and 667 predictions were obtained with a median prediction error of 0.03–0.76 min and interval width of 0.33–8.78 min. An external validation test of eight CSs showed high prediction accuracy. RT prediction was dependent on shape and type of LC gradient, and number of commonly measured compounds. Our study highlights PredRet’s accuracy and ability to transpose RT data acquired from one CS to another CS. We recommend extensive RT data sharing in PredRet by the community interested in plant food bioactive metabolites to achieve a powerful community-driven open-access tool for metabolomics annotation.