**1. Introduction**

There is no doubt that soybean [*Glycine max* (L.) Merrill] has a global importance with wide‐ spread applicability (food, biodiesel, secondary metabolites, among others) and economic value of its products in the global market [1] (*ca*. US\$ 38.9 billion is the estimated crop value in 2010 [2]). In terms of crop production, USA and Brazil occupy the first and second posi‐ tion in the world, with *ca*. 83 and 70 million ton, respectively [3]. These facts may explain the significant interest by biotechnological industries and research institutes in enhancing some characteristics of this crop such as nutrient quality, resistance to pests, and other subjects.

One of the most effective processes for attaining this task is the genetic modification, and clearly the one conferring resistance to glyphosate (the number one selling herbicide world‐ wide since the 80's [4]) is considered the main soybean genetic modification. This process involves the insertion of a gene (cp4 EPSPS*:* 5-enolpyruvylshikimate-3 phosphate synthase), via biobalistic (acceleration of metallic particles recovered with genetic material), which is responsible to the production of cp4-EPSPS enzyme from *Agrobacterium sp*. Such enzyme confers tolerance to glyphosate (N-fosfometil glycine), once that this substance inhibits the action of 5-enolpyruvylshiquimate synthase – EPSPS enzyme, which is involved in the bio‐

© 2013 Arruda et al.; licensee InTech. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2013 Arruda et al.; licensee InTech. This is a paper distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

synthesis of aromatic amino acids. Its inhibition provokes delay in the development of plants, amino acids unbalance, and death of plants [5]. As a consequence it is easy to ration‐ alize that plants genetically modified can normally develop in the presence of this herbicide, being the excellent result obtained in terms of soybean crop production also attributed to the transgenic cultures used. Exemplifying, *ca*. 49 million hectares (60% of the cultivated world area) are occupied nowadays by transgenic soybean culture [6].

In this way, our hypothesis is that the genetic modification itself is contributing for changing a variety of characteristics of this organism, producing alterations, in a cascade manner, to the metabolism. As a result of these modifications, the genetically modified soybean is appa‐ rently searching a new equilibrium as a living organism in nature.

In order to evaluate this hypothesis, our research group has been, for the last eight years, carry‐ ing out some comparative studies taking into account alterations in proteins, metalloproteins, metals and enzymes. Since the content of proteins in soybean seeds is high (*ca*. 40%) [7], hun‐ dreds of proteins are expected to be found after a separation process, making our proposal a hard task. Then, the utilization of the most up-to-date analytical techniques presenting high resolu‐ tion in terms of enzymes, proteomics and metallomics approaches is almost imperative.

In this chapter, the concept of plant stress is mainly one related to oxidative stress, followed by a variety of examples regarding soybean. Additionally, basic concepts of proteomics and metallomics will be described, followed by a compilation of the results from all strategies and techniques that we have been adopting along the period devoted to the study of trans‐ genic soybean, which were utilized for corroborating our previous hypothesis. Other exam‐ ples in the literature are also presented in order to support our data. Then, techniques based on bidimensional chromatographic and non-chromatographic protein separations (*i.e.* 2D-HPLC, 2D PAGE), image analysis for protein expression evaluations (*i.e.* 2D DIGE), inorgan‐ ic mass spectrometry for identification/quantification of metals (*i.e.* HR-SF-ICP-MS, ICP-MS, LA-ICP-MS), organic mass spectrometry for characterization of proteins (*i.e.* MALDI-QTOF-MS, ESI-LC-MS-MS), and hyphenated techniques for improving the quality on protein infor‐ mation (*i.e.* 2D-HPLC-ICP-MS) will be also emphasized. In the end of this chapter, a section of future Trends is provided, putting in evidence, in our point of view, some other strategies to be adopted for an in-depth investigation of this transgenic crop.

Finally, it is important to stress that the main goal of this chapter, and also of our studies, is only to present those results found within a series of projects developed by our research group concerning transgenic soybean. Despite the awareness of a public disagreement about the cultivation and commercialization of transgenic soybean, this chapter does not have the intention neither to defend genetic modification nor to make any criticisms to it.
