Abstract
While reviewing the plant proteomics topic, both from a conceptual and methodological point of view and with a historical perspective, recent advances, current states, challenges, and future directions of the field are discussed. Proteomics is moving, even though very slowly, from the descriptive era to a new era in which data start to be validated and integrated with other classic and -omics approaches, in the Systems Biology direction. This review is organized in different sections, starting with a general and historical introduction, moving to platforms and techniques employed currently, data validation to confidently conclude from a biological point of view, workflow in a multi-omics experiment, highlighting some illustrative investigations, and finishing with some conclusions and remarks. As quite reviews have been already published in the field of mass spectrometry-based proteomics and to avoid being repetitive, this review only reports the most relevant contributions published recently by our research groups and those found in the literature.
Communicated by Francisco M. Cánovas
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References
Abril N, Gion JM, Kerner R, Muller-Starck G, Cerrillo RM, Plomion C et al (2011) Proteomics research on forest trees, the most recalcitrant and orphan plant species. Phytochemistry 72:1219–1242. https://doi.org/10.1016/j.phytochem.2011.01.005
Aderem A (2005) Systems biology: its practice and challenges. Cell 121:511–513. https://doi.org/10.1016/j.cell.2005.04.020
Agarwal P, Parida SK, Mahto A, Das S, Mathew IE, Malik N, Tyagi AK (2014) Expanding frontiers in plant transcriptomics in aid of functional genomics and molecular breeding. Biotechnol J 9:1480–1492. https://doi.org/10.1002/biot.201400063
Aguilar-Hernandez V, Loyola-Vargas VM (2018) Advanced proteomic approaches to elucidate somatic embryogenesis. Front Plant Sci 9:1658. https://doi.org/10.3389/fpls.2018.01658
Alomirah HF, Allia I, Konishib Y (2000) Applications of mass spectrometry to food proteins and peptides. J Chromatogr A 893:1–21. https://doi.org/10.1016/S0021-9673(00)00745-7
Ambrosino L, Colantuono C, Monticolo F, Chiusano ML (2017) Bioinformatics resources for plant genomics: opportunities and bottlenecks in the -omics era. In: Bhadauria V (ed) Next-generation sequencing and bioinformatics for plant science. Caister Academic Press, Norfolk, pp 71–88. https://doi.org/10.21775/9781910190654.05
Amiour N, Imbaud S, Clement G, Agier N, Zivy M, Valot B et al (2012) The use of metabolomics integrated with transcriptomic and proteomic studies for identifying key steps involved in the control of nitrogen metabolism in crops such as maize. J Exp Bot 63:5017–5033. https://doi.org/10.1093/jxb/ers186
Arruda SC, Barbosa Hde S, Azevedo RA, Arruda MA (2011) Two-dimensional difference gel electrophoresis applied for analytical proteomics: fundamentals and applications to the study of plant proteomics. Analyst 136:4119–4126. https://doi.org/10.1039/c1an15513j
Arsova B, Watt M, Usadel B (2018) Monitoring of plant protein post-translational modifications using targeted proteomics. Front Plant Sci 9:1168. https://doi.org/10.3389/fpls.2018.01168
Baginsky S, Gruissem W (2006) Arabidopsis thaliana proteomics: from proteome to genome. J Exp Bot 57:1485–1491. https://doi.org/10.1093/jxb/erj130
Bakalarski CE, Haas W, Dephoure NE, Gygi SP (2007) The effects of mass accuracy, data acquisition speed, and search algorithm choice on peptide identification rates in phosphoproteomics. Anal Bioanal Chem 389:1409–1419. https://doi.org/10.1007/s00216-007-1563-x
Balcke GU, Bennewitz S, Bergau N, Athmer B, Henning A, Majovsky P et al (2017) Multi-omics of tomato glandular trichomes reveals distinct features of central carbon metabolism supporting high productivity of specialized metabolites. Plant Cell 29:960–983. https://doi.org/10.1105/tpc.17.00060
Balmer A, Pastor V, Gamir J, Flors V, Mauch-Mani B (2015) The ‘prime-ome’: towards a holistic approach to priming. Trends Plant Sci 20:443–452. https://doi.org/10.1016/j.tplants.2015.04.002
Barros E, Lezar S, Anttonen MJ, van Dijk JP, Rohlig RM, Kok EJ, Engel KH (2010) Comparison of two GM maize varieties with a near-isogenic non-GM variety using transcriptomics, proteomics and metabolomics. Plant Biotechnol J 8:436–451. https://doi.org/10.1111/j.1467-7652.2009.00487.x
Batista ANL, Santos-Pinto J, Batista JM Jr, Souza-Moreira TM, Santoni MM, Zanelli CF et al (2017) The combined use of proteomics and transcriptomics reveals a complex secondary metabolite network in Peperomia obtusifolia. J Nat Prod 80:1275–1286. https://doi.org/10.1021/acs.jnatprod.6b00827
Bauer M, Ahrne E, Baron AP, Glatter T, Fava LL, Santamaria A et al (2014) Evaluation of data-dependent and -independent mass spectrometric workflows for sensitive quantification of proteins and phosphorylation sites. J Proteome Res 13:5973–5988. https://doi.org/10.1021/pr500860c
Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J et al (2004) Potential of metabolomics as a functional genomics tool. Trends Plant Sci 9:418–425. https://doi.org/10.1016/j.tplants.2004.07.004
Blein-Nicolas M, Zivy M (2016) Thousand and one ways to quantify and compare protein abundances in label-free bottom-up proteomics. Biochim Biophys Acta 1864:883–895. https://doi.org/10.1016/j.bbapap.2016.02.019
Bolger ME, Weisshaar B, Scholz U, Stein N, Usadel B, Mayer KF (2014) Plant genome sequencing - applications for crop improvement. Curr Opin Biotechnol 26:31–37. https://doi.org/10.1016/j.copbio.2013.08.019
Calderon-Gonzalez KG, Hernandez-Monge J, Herrera-Aguirre ME, Luna-Arias JP (2016) Bioinformatics tools for proteomics data interpretation. Adv Exp Med Biol 919:281–341. https://doi.org/10.1007/978-3-319-41448-5_16
Calvete JJ (2014) The expanding universe of mass analyzer configurations for biological analysis. In: Jorríın JV (ed) Plant proteomics: methods and protocols, methods in molecular biology. Springer, New York, pp 61–81. https://doi.org/10.1007/978-1-62703-631-3_6
Cánovas FM, Dumas-Gaudot E, Recorbet G, Jorrín-Novo JV, Mock H-P, Rossignol M (2004) Plant proteome analysis. Proteomics 4:285–298. https://doi.org/10.1002/pmic.200300602
Carpentier SC, Panis B, Vertommen A, Swennen R, Sergeant K, Renaut J et al (2008) Proteome analysis of non-model plants: a challenging but powerful approach. Mass Spectrom Rev 27:354–377. https://doi.org/10.1002/mas.20170
Chang WWP, Huang L, Shen M, Webster C, Burlingame AL, Roberts JKM (2000) Patterns of protein synthesis and tolerance of anoxia in root tips of maize seedlings acclimated to a low-oxygen environment, and identification of proteins by mass spectrometry. Plant Physiol 122:295–317. https://doi.org/10.1104/pp.122.2.295
Chapman JD, Goodlett DR, Masselon CD (2014) Multiplexed and data-independent tandem mass spectrometry for global proteome profiling. Mass Spectrom Rev 33:452–470. https://doi.org/10.1002/mas.21400
Chen L (2017) Bioinformatics analysis of protein secretion in plants. In: Jiang L (ed) Plant protein secretion: methods and protocols, methods in molecular biology, vol 1662. Springer, New York, pp 33–43. https://doi.org/10.1007/978-1-4939-7262-3_3
Chen S, Harmon AC (2006) Advances in plant proteomics. Proteomics 6:5504–5516. https://doi.org/10.1002/pmic.200600143
Cho K, Shibato J, Agrawal GK, Jung YH, Kubo A, Jwa NS et al (2008) Integrated transcriptomics, proteomics, and metabolomics analyses to survey ozone responses in the leaves of rice seedling. J Proteome Res 7:2980–2998. https://doi.org/10.1021/pr800128q
Corpillo D, Gardini G, Vaira AM, Basso M, Aime S, Accotto GP et al (2004) Proteomics as a tool to improve investigation of substantial equivalence in genetically modified organisms: the case of a virus-resistant tomato. Proteomics 4:193–200. https://doi.org/10.1002/pmic.200300540
Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K (2011) Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol 11:163. https://doi.org/10.1186/1471-2229-11-163
Decourcelle M, Perez-Fons L, Baulande S, Steiger S, Couvelard L, Hem S et al (2015) Combined transcript, proteome, and metabolite analysis of transgenic maize seeds engineered for enhanced carotenoid synthesis reveals pleotropic effects in core metabolism. J Exp Bot 66:3141–3150. https://doi.org/10.1093/jxb/erv120
Demir F, Niedermaier S, Villamor JG, Huesgen PF (2018) Quantitative proteomics in plant protease substrate identification. New Phytol 218:936–943. https://doi.org/10.1111/nph.14587
Edwards D, Batley J (2004) Plant bioinformatics: from genome to phenome. Trends Biotechnol 22:232–237. https://doi.org/10.1016/j.tibtech.2004.03.002
Egorov TA, Musolyamov AK, Andersen JS, Roepstorff P (1994) The complete amino acid sequence and disulphide bond arrangement of oat alcohol-soluble avenin-3. Eur J Biochem 224:631–638. https://doi.org/10.1111/j.1432-1033.1994.00631.x
Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64–71. https://doi.org/10.1126/science.2675315
Fernie AR, Stitt M (2012) On the discordance of metabolomics with proteomics and transcriptomics: coping with increasing complexity in logic, chemistry, and network interactions scientific correspondence. Plant Physiol 158:1139–1145. https://doi.org/10.1104/pp.112.193235
Flexas J, Gago J (2018) A role for ecophysiology in the ‘omics’ era. Plant J 96:251–259. https://doi.org/10.1111/tpj.14059
Friso G, Giacomelli L, Ytterberg AJ, Peltier JB, Rudella A, Sun Q et al (2004) In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database. Plant Cell 16:478–499. https://doi.org/10.1105/tpc.017814
Fukushima A, Kusano M, Redestig H, Arita M, A Saito K (2009) Integrated omics approaches in plant systems biology. Curr Opin Chem Biol 13:532–538. https://doi.org/10.1016/j.cbpa.2009.09.022
Fukushima A, Kanaya S, Nishida K (2014) Integrated network analysis and effective tools in plant systems biology. Front Plant Sci 5:598. https://doi.org/10.3389/fpls.2014.00598
Galland M, He D, Lounifi I, Arc E, Clement G, Balzergue S et al (2017) An integrated “multi-omics” comparison of embryo and endosperm tissue-specific features and their impact on rice seed quality. Front Plant Sci 8:1984. https://doi.org/10.3389/fpls.2017.01984
Gardinassi LG, Xia J, Safo SE, Li S (2017) Bioinformatics tools for the interpretation of metabolomics data. Curr Pharmacol Rep 3:374–383. https://doi.org/10.1007/s40495-017-0107-0
Ghan R, Van Sluyter SC, Hochberg U, Degu A, Hopper DW, Tillet RL et al (2015) Five omic technologies are concordant in differentiating the biochemical chracteristics of the berries of five grapevine (Vitis vinifera L.) cultiars. BMC Genomics 16:946
Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L et al (2012) Targeted data extraction of the MS/MS spectra generated by data independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 11:O111.016717. https://doi.org/10.1074/mcp.O111.016717
Gomez-Casati DF, Busi MV, Barchiesi J, Peralta DA, Hedin N, Bhadauria V (2018) Applications of bioinformatics to plant biotechnology. Curr Issues Mol Biol 27:89–104. https://doi.org/10.21775/9781910190654.06
Gonzalez-Fernandez R, Aloria K, Arizmendi JM, Jorrín-Novo JV (2013) Application of label-free shotgun nUPLC-MS(E) and 2-DE approaches in the study of Botrytis cinerea mycelium. J Proteome Res 12:3042–3056. https://doi.org/10.1021/pr3010937
Großkinsky DK, Syaiafullah SJ, Roitsch T (2018) Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants. J Exp Bot 69:825–844. https://doi.org/10.1093/jxb/erx333
Guerrero-Sanchez VM, Maldonado-Alconada AM, Amil-Ruiz F, Jorrín-Novo JV (2017) Holm oak (Quercus ilex) transcriptome. De novo sequencing and assembly analysis. Front Mol Biosci 4:70. https://doi.org/10.3389/fmolb.2017.00070
Guerrero-Sanchez VM, Maldonado-Alconada AM, Amil-Ruiz F, Verardi A, Jorrín-Novo JV, Rey MD (2019) Ion Torrent and Illumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptome. PLoS One 14:e0210356. https://doi.org/10.1371/journal.pone.0210356
Gunnigle E, Ramond JB, Frossard A, Seeley M, Cowan D (2014) A sequential co-extraction method for DNA, RNA and protein recovery from soil for future system-based approaches. J Microbiol Methods 103:118–123. https://doi.org/10.1016/j.mimet.2014.06.004
Hall RD (2006) Plant metabolomics: from holistic hope, to hype, to hot topic. New Phytol 169:453–468. https://doi.org/10.1111/j.1469-8137.2005.01632.x
Hasin Y, Seldin M, Lusis A (2017) Multi-omics approaches to disease. Genome Biol 18:83. https://doi.org/10.1186/s13059-017-1215-1
Hennig L (2007) Patterns of beauty-omics meets plant development. Trends Plant Sci 12:287–293. https://doi.org/10.1016/j.tplants.2007.05.002
Holtorf H, Guitton MC, Reski R (2002) Plant functional genomics. Naturwissenschaften 89:235–249. https://doi.org/10.1007/s00114-002-0321-3
Jansson S, Douglas CJ (2007) Populus: a model system for plant biology. Annu Rev Plant Biol 58:435–458. https://doi.org/10.1146/annurev.arplant.58.032806.103956
Jorrín JV (2015) Scientific standards and MIAPEs in plant proteomics research and publications. Front Plant Sci 6:473. https://doi.org/10.3389/fpls.2015.00473
Jorrín-Novo JV (2014) Plant proteomics methods and protocols. In: Jorríın JV (ed) Plant proteomics: methods and protocols, methods in molecular biology. Springer, New York, pp 3–13. https://doi.org/10.1007/978-1-62703-631-3_1
Jorrín-Novo JV, Valledor L (2013) Translational proteomics special issue. J Proteome 93:1–4. https://doi.org/10.1016/j.jprot.2013.10.019
Jorrín-Novo JV, Maldonado-Alconada AM, Castillejo MA (2007) Plant proteome analysis: a 2006 update. Proteomics 7:2947–2962. https://doi.org/10.1002/pmic.200700135
Jorrín-Novo JV, Maldonado AM, Echevarría-Zomeño S, Valledor L, Castillejo MA, Curto M et al (2009) Plant Proteomics update (2007-2008). Second-generation proteomic techniques, an appropriate experimental design, and data analysis methods that meet MIAPE standards, increase plant proteome coverage and expand biological knowledge. J Proteome 72:285–314. https://doi.org/10.1016/j.jprot.2009.01.026
Jorrín-Novo JV, Pascual J, Sanchez-Lucas R, Romero-Rodriguez MC, Rodriguez-Ortega MJ, Lenz C et al (2015) Fourteen years of plant proteomics reflected in Proteomics: moving from model species and 2DE-based approaches to orphan species and gel-free platforms. Proteomics 15:1089–1112. https://doi.org/10.1002/pmic.201400349
Jorrín-Novo JV, Komatsu S, Sanchez-Lucas R, Rodriguez de Francisco LE (2018) Gel electrophoresis-based plant proteomics: past, present, and future. Happy 10th anniversary Journal of Proteomics! J Proteome 198:1–10. https://doi.org/10.1016/j.jprot.2018.08.016
Joyce AR, Palsson BO (2006) The model organism as a system: integrating ‘omics’ data sets. Nat Rev Mol Cell Biol 7:198–210. https://doi.org/10.1038/nrm1857
Kapazoglou A, Ganopoulos I, Tani E, Tsaftaris A (2018) Epigenetics, epigenomics and crop improvement. In: Kuntz M (ed) Advances in botanical research. Elsevier, Amsterdam, pp 287–324. https://doi.org/10.1016/bs.abr.2017.11.007
Kehr J, Haebel S, Blechschmidt-Schneider S, Willmitzer L, Steup M, Fisahn J (1999) Analysis of phloem protein patterns from different organs of Cucurbita maxima Duch. by matrix-assisted laser desorption/ionization time of flight mass spectroscopy combined with sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Planta 207:612–619. https://doi.org/10.1007/s004250050525
Kim M, Tagkopoulos I (2018) Data integration and predictive modeling methods for multi-omics datasets. Mol Omics 14:8–25. https://doi.org/10.1039/C7MO00051K
Kim ST, Kim SG, Agrawal GK, Kikuchi S, Rakwal R (2014) Rice proteomics: a model system for crop improvement and food security. Proteomics 14:593–610. https://doi.org/10.1002/pmic.201300388
Kim SW, Gupta R, Lee SH, Min CW, Agrawal GK, Rakwal R et al (2016a) An integrated biochemical, proteomics, and metabolomics approach for supporting medicinal value of panax ginseng fruits. Front Plant Sci 7:994. https://doi.org/10.3389/fpls.2016.00994
Kim J, Woo HR, Nam HG (2016b) Toward systems understanding of leaf senescence: an integrated multi-omics perspective on leaf senescence research. Mol Plant 9:813–825. https://doi.org/10.1016/j.molp.2016.04.017
Kitano H (2002) Systems biology: a brief overview. Science 295:1662–1664. https://doi.org/10.1126/science.1069492
Klabunde T, Stahl B, Suerbaum H, Hahner S, Karas M, Hillenkamp F et al (1994) The amino acid sequence of the red kidney bean Fe(II1)-Zn(I1) purple acid phosphatase. Eur J Biochem 226:369–375. https://doi.org/10.1111/j.1432-1033.1994.tb20061.x
Kohler C, Springer N (2017) Plant epigenomics-deciphering the mechanisms of epigenetic inheritance and plasticity in plants. Genome Biol 18:132. https://doi.org/10.1186/s13059-017-1260-9
Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M et al (2015) Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. Front Plant Sci 6:563. https://doi.org/10.3389/fpls.2015.00563
Koller A, Washbum MP, Lange BM, Andon NL, Deciu C, Haynes PA et al (2002) Proteomic survey of metabolic pathways in rice. Proc Natl Acad Sci 99:11969–11974. https://doi.org/10.1073/pnas.172183199
Komatsu S, Jorrín-Novo JV (2016) Food and crop proteomics. J Proteome 143:1–2. https://doi.org/10.1016/j.jprot.2016.07.004
Kosová K, Vítámvás P, Prášil IT, Renaut J (2011) Plant proteome changes under abiotic stress – contribution of proteomics studies to understanding plant stress response. J Proteome 74:1301–1322. https://doi.org/10.1016/j.jprot.2011.02.006
Kuehnbaum NL, Britz-McKibbin P (2013) New advances in separation science for metabolomics: resolving chemical diversity in a post-genomic era. Chem Rev 113:2437–2468. https://doi.org/10.1021/cr300484s
Lau BYC, Othman A, Ramli US (2018) Application of proteomics technologies in oil palm research. Protein J 37:473–499. https://doi.org/10.1007/s10930-018-9802-x
Law KP, Lim YP (2013) Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring. Expert Rev Proteomics 10:551–566. https://doi.org/10.1586/14789450.2013.858022
Leonavicius K, Nainys J, Kuciauskas D, Mazutis L (2019) Multi-omics at single-cell resolution: comparison of experimental and data fusion approaches. Curr Opin Biotechnol 55:159–166. https://doi.org/10.1016/j.copbio.2018.09.012
Li J, Assmann SM (2000) Mass spectrometry an essential tool in proteome analysis. Plant Physiol 123:807–809. https://doi.org/10.1104/pp.123.3.807
Li J, Ren L, Gao Z, Jiang M, Liu Y, Zhou L et al (2017) Combined transcriptomic and proteomic analysis constructs a new model for light-induced anthocyanin biosynthesis in eggplant (Solanum melongena L.). Plant Cell Environ 40:3069–3087. https://doi.org/10.1111/pce.13074
Liang C, Cheng S, Zhang Y, Sun Y, Fernie AR, Kang K et al (2016) Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination. BMC Plant Biol 16:43. https://doi.org/10.1186/s12870-016-0726-3
Liu F, Marshall RS, Li F (2018) Understanding and exploiting the roles of autophagy in plants through multi-omics approaches. Plant Sci 274:146–152. https://doi.org/10.1016/j.plantsci.2018.05.009
López-Hidalgo C, Guerrero-Sanchez VM, Gomez-Galvez I, Sanchez-Lucas R, Castillejo-Sanchez MA, Maldonado-Alconada AM et al (2018) A multi-omics analysis pipeline for the metabolic pathway reconstruction in the orphan species Quercus ilex. Front Plant Sci 9:935. https://doi.org/10.3389/fpls.2018.00935
Lyon D, Weckwerth W, Wienkoop S (2014) Mass Western for absolute quantification of target proteins and considerations about the instrument of choice. In: Jorríın JV (ed) Plant proteomics: methods and protocols, methods in molecular biology. Springer, New York, pp 199–208. https://doi.org/10.1007/978-1-62703-631-3_15
Mann M (2008) Can proteomics retire the western blot? J Proteome Res 7:3065. https://doi.org/10.1021/pr800463v
Manzoni C, Kia DA, Vandrovcova J, Hardy J, Wood NW, Lewis PA et al (2016) Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. Brief Bioinform 19:286–302. https://doi.org/10.1093/bib/bbw114
Matthiesen R (2007) Methods, algorithms and tools in computational proteomics: a practical point of view. Proteomics 7:2815–2832. https://doi.org/10.1002/pmic.200700116
Mensack MM, Fitzgerald VK, Ryan EP, Lewis MR, Thompson HJ, Brick MA (2010) Evaluation of diversity among common beans (Phaseolus vulgaris L.) from two centers of domestication using ‘omics’ technologies. BMC Genomics 11:686. https://doi.org/10.1186/1471-2164-11-686
Mirzaei H, Carrasco M (2016) Advances in experimental medicine and biology. In: Modern proteomics–sample preparation, analysis and practical applications. Springer, Cham. https://doi.org/10.1007/978-3-319-41448-5
Misra BB (2018) Updates on resources, software tools, and databases for plant proteomics in 2016-2017. Electrophoresis 39:1543–1557. https://doi.org/10.1002/elps.201700401
Mochida K, Shinozaki K (2011) Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant Cell Physiol 52:2017–2038. https://doi.org/10.1093/pcp/pcr153
Muller B, Grossniklaus U (2010) Model organisms - a historical perspective. J Proteome 73:2054–2063. https://doi.org/10.1016/j.jprot.2010.08.002
Natera SHA, Guerreiro N, Djordjevic MA (2000) Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis. Mol Plant-Microbe Interact 13:995–1009. https://doi.org/10.1094/MPMI.2000.13.9.995
Neilson KA, Ali NA, Muralidharan S, Mirzaei M, Mariani M, Assadourian G et al (2011) Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 11:535–553. https://doi.org/10.1002/pmic.201000553
Park OMK (2004) Proteomic studies in plants. BMB Rep 37:133–138
Peltier J-B, Friso G, Kalume DE, Roepstorff P, Nilsson F, Adamska I et al (2000) Proteomics of the chloroplast: systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins. Plant Cell 12:319–341. https://doi.org/10.1105/tpc.12.3.319
Picotti P, Bodenmiller B, Aebersold R (2013) Proteomics meets the scientific method. Nat Methods 10:24–27. https://doi.org/10.1038/nmeth.2291
Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C et al (2016) Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Resour 16:254–265. https://doi.org/10.1111/1755-0998.12425
Potters G (2010) Systems biology of the cell. Nat Educ 3:33
Proust H, Hartmann C, Crespi M, Lelandais-Briere C (2018) Root development in Medicago truncatula: lessons from genetics to functional genomics. In: Cañas LA, Beltrán JP (eds) Methods and protocols, methods in molecular biology, vol 1822. Springer, New York, pp 205–239. https://doi.org/10.1007/978-1-4939-8633-0_15
Qin L, Zhang Y, Liu Y, He H, Han M, Li Y et al (2018) Recent advances in matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) for in situ analysis of endogenous molecules in plants. Phytochem Anal 29:351–364. https://doi.org/10.1002/pca.2759
Rajasundaram D, Selbig J (2016) More effort – more results: recent advances in integrative ‘omics’ data analysis. Curr Opin Plant Biol 30:57–61. https://doi.org/10.1016/j.pbi.2015.12.010
Ramos AM, Usie A, Barbosa P, Barros PM, Capote T, Chaves I et al (2018) The draft genome sequence of cork oak. Sci Data 5:180069. https://doi.org/10.1038/sdata.2018.69
Rey MD, Castillejo MA, Sanchez-Lucas R, Guerrero-Sanchez VM, Lopez-Hidalgo C, Romero-Rodriguez C et al (2019) Proteomics, Holm oak (Quercus ilex L.) and other recalcitrant and orphan forest tree species: how do they see each other? Int J Mol Sci 20:692. https://doi.org/10.3390/ijms20030692
Ricroch AE, Berge JB, Kuntz M (2011) Evaluation of genetically engineered crops using transcriptomic, proteomic, and metabolomic profiling techniques. Plant Physiol 155:1752–1761. https://doi.org/10.1104/pp.111.173609
Ritchie SC, Würtz P, Nath AP, Abraham G, Havulinna AS, Fearnley LG et al (2015) The biomarker GlycA is associated with chronic inflammation and predicts long-term risk of severe infection. Cell Syst 1:293–301. https://doi.org/10.1016/j.cels.2015.09.007
Rose JK, Bashir S, Giovannoni JJ, Jahn MM, Saravanan RS (2004) Tackling the plant proteome: practical approaches, hurdles and experimental tools. Plant J 39:715–733. https://doi.org/10.1111/j.1365-313X.2004.02182.x
Rossignol M, Peltier J-B, Mock H-P, Matros A, Maldonado AM, Jorrín-Novo JV (2006) Plant proteome analysis: a 2004–2006 update. Proteomics 6:5529–5548. https://doi.org/10.1002/pmic.200600260
Roume H, Heintz-Buschart A, Muller EE, Wilmes P (2013) Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample. In: Methods in enzymology, vol 531. Academic Press, Cambridge, pp 219–236
Sakata K, Komatsu S (2014) Plant proteomics: from genome sequencing to proteome databases and repositories. In: Jorríın JV (ed) Plant proteomics: methods and protocols, methods in molecular biology. Springer, New York, pp 29–42. https://doi.org/10.1007/978-1-62703-631-3_3
Sambrook J, Russel DW (2006) Purification of nucleic acids by extraction with phenol: chloroform. CSH Protoc 2006(1). https://doi.org/10.1101/pdb.prot4455
Sanchez-Lucas R, Mehta A, Valledor L, Cabello-Hurtado F, Romero-Rodriguez MC, Simova-Stoilova L et al (2016) A year (2014-2015) of plants in Proteomics Journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists. Proteomics 16:866–876. https://doi.org/10.1002/pmic.201500351
Sankaranarayanan S, Jamshed M, Samuel MA (2013) Proteomics approaches advance our understanding of plant self-incompatibility response. J Proteome Res 12:4717–4726. https://doi.org/10.1021/pr400716r
Schulze WX, Usadel B (2010) Quantitation in mass-spectrometry-based proteomics. Annu Rev Plant Biol 61:491–516. https://doi.org/10.1146/annurev-arplant-042809-112132
Singh S, Parihar P, Singh R, Singh VP, Prasad SM (2016) Heavy metal tolerance in plants: role of transcriptomics, proteomics, metabolomics, and ionomics. Front Plant Sci 6:1143. https://doi.org/10.3389/fpls.2015.01143
Singh A, Shannon CP, Gautier B, Rohart F, Vacher M, Tebbutt SJ et al (2019) DIABLO: an integrative approach for identifying key molecular drivers from multi-omic assays. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty1054
Sork VL, Fitz-Gibbon ST, Puiu D, Crepeau M, Gugger PF, Sherman R et al (2016) First draft assembly and annotation of the genome of a California endemic oak Quercus lobata Nee (Fagaceae). G3 (Bethesda) 6:3485–3495. https://doi.org/10.1534/g3.116.030411
Srivastava V, Obudulu O, Bygdell J, Löfstedt T, Rydén P, Nilsson R et al (2013) OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants. BMC Genomics 14:893. https://doi.org/10.1186/1471-2164-14-893
Stitt M, Gibon Y (2014) Why measure enzyme activities in the era of systems biology? Trends Plant Sci 19:256–265. https://doi.org/10.1016/j.tplants.2013.11.003
Suwabe K, Yano K (2008) Omics databases in plant science: key to systems biology. Plant Biotechnol 25:413–422. https://doi.org/10.5511/plantbiotechnology.25.413
Takac T, Samajova O, Samaj J (2017) Integrating cell biology and proteomic approaches in plants. J Proteome 169:165–175. https://doi.org/10.1016/j.jprot.2017.04.020
Tanaka K, Waki H, Ido Y, Akita S, Yoshida Y, Yoshida T (1988) Protein and polymer analyses up to mlz 100 000 by laser ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 2:151–153. https://doi.org/10.1002/rcm.1290020802
Thangaraj B, Ryan CM, Souda P, Krause K, Faull KF, Weber AP et al (2010) Data-directed top-down Fourier-transform mass spectrometry of a large integral membrane protein complex: photosystem II from Galdieria sulphuraria. Proteomics 10:3644–3656. https://doi.org/10.1002/pmic.201000190
Thelen JJ, Peck SC (2007) Quantitative proteomics in plants: choices in abundance. Plant Cell 19:3339–3346. https://doi.org/10.1105/tpc.107.053991
Thiellement H, Bahrman N, Damerval C, Plomion C, Rossignol M, Santoni V et al (1999) Proteomics for genetic and physiological studies in plants. Electrophoresis 20:2013–2026. https://doi.org/10.1002/(SICI)1522-2683(19990701)20:10<2013::AID-ELPS2013>3.0.CO;2-#
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR et al (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562. https://doi.org/10.1038/nprot.2012.016
Valledor L, Jorríın JV (2011) Back to the basics: maximizing the information obtained by quantitative two dimensional gel electrophoresis analyses by an appropriate experimental design and statistical analyses. J Proteome 74:1–18. https://doi.org/10.1016/j.jprot.2010.07.007
Valledor L, Escandón M, Meijón M, Nukarinen E, Cañal MJ, Weckwerth W (2014) A universal protocol from the combined isolation of metabolites, DNA, long RNAs, small RNAs, and proteins from plants and microorganisms. Plant J 79:173–180. https://doi.org/10.1111/tpj.12546
Valledor L, Carbó M, Lamelas L, Escandón M, Colina FJ, Cañal MJ et al (2018) When the tree let us see the forest: systems biology and natural variation studies in forest species. In: Progress in botany. Springer, New York, pp 345–367. https://doi.org/10.1007/124_2018_22
van den Berg RA, Hoefsloot HC, Westerhuis JA, Smilde AK, van der Werf MJ (2006) Centering, scaling, and transformations: improving the biological information content of metabolomics data. BMC Genomics 7:142. https://doi.org/10.1186/1471-2164-7-142
Varshney RK, Pandey MK, Chitikineni A (2018) Plant genetics and molecular biology: an introduction. Adv Biochem Eng Biotechnol 164:1–9. https://doi.org/10.1007/10_2017_45
Velez-Bermudez IC, Wen TN, Lan P, Schmidt W (2016) Isobaric tag for relative and absolute quantitation (iTRAQ)-based protein profiling in plants. In: Lois LM, Matthiesen R (eds) Plant proteostasis: methods and protocols, methods in molecular biology. Springer, New York, pp 213–221. https://doi.org/10.1007/978-1-4939-3759-2_17
Vijayakumar V, Liebisch G, Buer B, Xue L, Gerlach N, Blau S et al (2016) Integrated multi-omics analysis supports role of lysophosphatidylcholine and related glycerophospholipids in the Lotus japonicus–Glomus intraradices mycorrhizal symbiosis. Plant Cell Environ 39:393–415. https://doi.org/10.1111/pce.12624
Weckwerth W (2004) Metabolomics in systems biology. Annu Rev Plant Biol 54:669–689. https://doi.org/10.1146/annurev.arplant.54.031902.135014
Weckwerth W (2011) Green systems biology-from single genomes, proteomes and metabolomes to ecosystems research and biotechnology. J Proteome 75:284–305. https://doi.org/10.1016/j.jprot.2011.07.010
Whitelegge JP, Komatsu S, Jorrín-Novo JV (2011) Diverse facets of plant proteomics. Phytochemistry 72:961–962. https://doi.org/10.1016/j.phytochem.2011.04.004
Widjaja I, Naumann K, Roth U, Wolf N, Mackey D, Dangl JL et al (2009) Combining subproteome enrichment and Rubisco depletion enables identification of low abundance proteins differentially regulated during plant defense. Proteomics 9:138–147. https://doi.org/10.1002/pmic.200800293
Wilkins MR, Sánchez J-C, Gooley AA, Appel RD, Humphrey-Smith I, Hochstrasser DF, Williams KL (1996) Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 13:19–50. https://doi.org/10.1080/02648725.1996.10647923
Wisniewski JR, Mann M (2016) A proteomics approach to the protein normalization problem: selection of unvarying proteins for MS-based proteomics and western blotting. J Proteome Res 15:2321–2326. https://doi.org/10.1021/acs.jproteome.6b00403
Xing S, Wallmeroth N, Berendzen KW, Grefen C (2016) Techniques for the analysis of protein-protein interactions in vivo. Plant Physiol 171:727–758. https://doi.org/10.1104/pp.16.00470
Xiong J, Yang Q, Kang J, Sun Y, Zhang T, Margaret G et al (2011) Simultaneous isolation of DNA, RNA, and protein from Medicago truncatula L. Electrophoresis 32:321–330. https://doi.org/10.1002/elps.201000425
Yuan JS, Galbraith DW, Dai SY, Griffin P, Stewart CN Jr (2008) Plant systems biology comes of age. Trends Plant Sci 13:165–171. https://doi.org/10.1016/j.tplants.2008.02.003
Zhang H, Cui W, Wen J, Blankenship RE, Gross ML (2011) Native electrospray and electron-capture dissociation FTICR mass spectrometry for top-down studies of protein assemblies. Anal Chem 83:5598–5606. https://doi.org/10.1021/ac200695d
Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR III (2013) Protein analysis by shotgun/bottom up proteomics. Chem Rev 113:2343–2394. https://doi.org/10.1021/cr3003533
Zhu FY, Chen MX, Chan WL, Yang F, Tian Y, Song T et al (2018) SWATH-MS quantitative proteomic investigation of nitrogen starvation in Arabidopsis reveals new aspects of plant nitrogen stress responses. J Proteome 187:161–170. https://doi.org/10.1016/j.jprot.2018.07.014
Zivy M, Wienkoop S, Renaut J, Pinheiro C, Goulas E, Carpentier S (2015) The quest for tolerant varieties: the importance of integrating “omics” techniques to phenotyping. Front Plant Sci 6:448. https://doi.org/10.3389/fpls.2015.0044
Acknowledgments
The authors thank University of Córdoba (UCO-CeiA3) and the staff of the Central Service for Research Support (SCAI) at the University of Córdoba (Spain) for its technical support in the bioinformatics data analysis. This research was supported by the grant ENCINOMICA BIO2015-64737-R from Spanish Ministry of Economy and Competitiveness. MD-R thanks the contract “Ayudas Juan de la Cierva-Formación (FJCI-2016-28296)” of the Spanish Ministry of Science, Innovation and Universities. MAC thanks the contract “Ramón y Cajal Fellowship (RYC-2017-23706)” of the Spanish Ministry of Science, Innovation and Universities. RSL thanks the contract “FPU14/00186” of the Spanish Ministry of Science, Innovation and Universities.
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Rey, MD. et al. (2019). Recent Advances in MS-Based Plant Proteomics: Proteomics Data Validation Through Integration with Other Classic and -Omics Approaches. In: Cánovas, F., Lüttge, U., Leuschner, C., Risueño, MC. (eds) Progress in Botany Vol. 81. Progress in Botany, vol 81. Springer, Cham. https://doi.org/10.1007/124_2019_32
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