Membrane proteomics: Use of additive main effects with multiplicative interaction model to classify plasma membrane proteins according to their solubility and electrophoretic properties
Authors: D Desclaux
T Rabilloud
S Kieffer
F Masson
V Santoni
Journal: Electrophoresis (2000)
Discipline: CHEMISTRY
Keywords: proteomic level; plasma membrane; Arabidopsis thaliana; hydrophobic proteins; two-dimensional electrophoresis gels

Abstract:  Recent efforts at the proteomic level were employed to describe the protein equipment of the plasma membrane of the model plant Arabidopsis thaliana. These studies had revealed that the plasma membrane is rich in extrinsic proteins but came up against two major problems: (i) few hydrophobic proteins were recovered in two-dimensional electrophoresis gels, and (ii) many plasma membrane proteins had no known function or were unknown in the database despite extensive sequencing of the Arabidopsis genome. In this paper, several methods expected to enrich a membrane sample in hydrophobic proteins were compared. The optimization of solubilization procedures revealed that the detergent to be used depends on the lipid content of the sample. The corresponding proteomes were compared with the statistical model AMMI (additive main effects with multiplicative interaction) that aimed at regrouping proteins according to their solubility and electrophoretic properties. Distinct groups emerged from this analysis and the identification of proteins in each group allowed us to assign specific features to several of them. For instance, two of these groups regrouped very hydrophobic proteins, one group contained V-ATPase subunits, another group contained proteins with one transmembrane domain as well as proteins known to interact with membrane proteins. This study provides methodological tools to study particular classes of plasma membrane proteins and should be applicable to other cellular membranes. 

Retracted: No

PubPeer comments:
 Figure 3a, panel duplication (red boxes):  , 
 We, Dr Santoni and Dr Rabilloud, received a message suggesting that there is an image duplication in one figure of our study published in Electrophoresis (2000s) vol 21 pages 3329-3344. As a technical point of view, the image represents a blot that has been probed with an ATPase antibody (the upper image) in an upper portion of the blot (MW ca. 90 kDa) and with an actin antibody (lower image) in a lower portion of the blot (MW ca. 40 kDa). Instead of providing an image analysis that could be perceived as a pro domo justification, we would rather like to invite interested scientists to download the version of record from the publisheru2019s website, to go to the targeted figure and to use a high enough magnification to go into the details of both panels. Technical elements that are well-known of practitioners of SDS electrophoresis and western blotting can then be measured on the images: -Width of the bands themselves. In SDS electrophoresis it is quite common that the bands get larger in the same lane from the top of the gel (high molecular weight) to the bottom of the gel (low molecular weight). -Inter-lane width. When a SDS gel is not loaded on all its lanes, the conductivity differences between the gel itself and the samples deform the electric field, resulting in a slightly deformed migration and thus an increase in the Inter-lane width, here again more pronounced from the top to the bottom of the gel. When adjacent lanes are used, the outermost lane(s) is (are) more prone to this phenomenon than the innermost lanes, which is consistent with the cause of the electric field deformation. -Fine structure of the bands. We mean by this wording both the detailed shape of the bands and the fine structure of the gray levels for each band. It should also be kept in mind that in SDS electrophoresis, when a lane gets some deformation, whatever it is, all the bands in this precise lane get similar deformation(s). Carrying out this exercise honestly shows that both images are consistent with the description of the experiment, i.e. two portions of the same gel probed by different antibodies. Both panels are very similar when examined at low magnification, which is consistent with their common origin from the same gel and thus shared band deformations, but show enough differences at a higher magnification to rebut any accusation of panel duplication. Dr Vu00e9ronique Santoni and Dr Thierry Rabilloud , 
 Thank you for your reply. I disagree. Shape of bands and their fine structure appear to be identical. Posted image in my comment #1 has been cropped from the original article. The size of Figure 3a is very small within the paper and its resolution is not the best possible, also due to the fact that the article is quite dated. Although the paper is 21 years old, if the authors still have the uncropped scan of the original blot at better resolution, they could post it here and take away any concern. ,