Assessment of heterogeneous molecular weight shift of proteins revealed by deep purple (DP) staining.

<p>The proteomic map has been labeled by Cy3 (green) and stained DP (red) (A). This process revealed a predominant shift of low molecular weight proteins, with the Cy3-labeled proteins appearing heavier than the DP-stained proteins (B). The shift seemed weaker and could even disappear in the case of higher molecular weight proteins (C) but this observation did not apply to all high MW proteins (D). Moreover, some proteins were stained only by Cy3 and others only by DP (arrows in E).</p

Fluorescence-based bidimensional immunoproteomic (FBIP) approach.

<p>In the FBIP procedure, 3 maps are generated from one 2D immunoblot (A–C). After 2-D electrophoresis of Cy3 labeled proteins (A), the immunoblotting is treated at the same time with a pool of commercially specific antibodies (landmark) and with human serum (antigenic map). The landmark is revealed with a set of Alexa Fluor 647-conjugated secondary antibodies (B). The antigenic map obtained with serum 1 is revealed with a horseradish peroxidase-conjugated anti-human antibody using chemifluorescence kit ECL PLUS (C). The direct superimposition of the 3 maps in the 3 wavelengths (D) revealed correct matching of reactivity towards ENOA (E) and a mismatch for reactivity against G3P (F). A defect of the superimposition was observed between the Cy3-labeled G3P protein and the corresponding mAb reactivity. The reproducibility of this approach is illustrated in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132142#pone.0132142.s003" target="_blank">S2 Fig</a>.</p

List of proteins identified by LTQ-ORBITRAP-Velos.

<p>^aSpot number according in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132142#pone.0132142.g004" target="_blank">Fig 4B2 and 4B3</a>.</p><p>^bAccession number and protein name according SwissProt.</p><p>^cIsoelectric point (pI) and molecular weight (MW): Theoretical (Theo) and Experimental (Exp).</p><p>List of proteins identified by LTQ-ORBITRAP-Velos.</p

Chemiluminescence-based bidimensional immunoproteomic approach.

<p>After bi-dimensional electrophoresis of HEp-2 protein extract, we performed immunoblotting with sera from 2 patients with autoimmune diseases, thereby generating 2 antigenic maps (A, serum 1 and serum 2). We performed another immunoblotting (landmark map, B) using commercially available monoclonal antibodies against ACTB, HSP71, ENOA, G3P and TPIS. This landmark allowed anchoring to be used to superimpose both the antigenic maps (A) and the colloidal blue-stained proteomic map (C). The yellow area highlights some of the reactivity diversity between the 2 sera. The red area highlights antigenic spots (A, serum 2) for which there are no corresponding protein spots on the CCB gel (C). Sizes of immunoblots/gel and molecular weight distribution are indicated, to point out the distortions between their respective derived images. The differences between the relative mobility of HSP71 and G3P were measured at 3.6, 3.3 and 5.3 cm, respectively with serum 1, serum 2 and on CCB gel.</p

An Optimized Fluorescence-Based Bidimensional Immunoproteomic Approach for Accurate Screening of Autoantibodies

<div><p>Serological proteome analysis (SERPA) combines classical proteomic technology with effective separation of cellular protein extracts on two-dimensional gel electrophoresis, western blotting, and identification of the antigenic spot of interest by mass spectrometry. A critical point is related to the antigenic target characterization by mass spectrometry, which depends on the accuracy of the matching of antigenic reactivities on the protein spots during the 2D immunoproteomic procedures. The superimposition, based essentially on visual criteria of antigenic and protein spots, remains the major limitation of SERPA. The introduction of fluorescent dyes in proteomic strategies, commonly known as 2D-DIGE (differential in-gel electrophoresis), has boosted the qualitative capabilities of 2D electrophoresis. Based on this 2D-DIGE strategy, we have improved the conventional SERPA by developing a new and entirely fluorescence-based bi-dimensional immunoproteomic (FBIP) analysis, performed with three fluorescent dyes. To optimize the alignment of the different antigenic maps, we introduced a landmark map composed of a combination of specific antibodies. This methodological development allows simultaneous revelation of the antigenic, landmark and proteomic maps on each immunoblot. A computer-assisted process using commercially available software automatically leads to the superimposition of the different maps, ensuring accurate localization of antigenic spots of interest.</p></div

Progenesis SameSpots assisted analysis of FBIP approach.

<p>For the analysis of the immunoblots, Progenesis SameSpots software begins by inter-gel alignment step (A). To rectify the defect of superimposition of the proteomic maps revealed on each immunoblot (A1), Progenesis SameSpots suggested correcting vectors (blue vectors in A2). This automatic alignment was improved by applying manual vectors (red vectors in A2) to obtain perfect spot alignment (A3). For the analysis of immune reactivity, Progenesis SameSpots software displays both 2D and 3D images of reactivity associated with protein spots (B). The verification of the co-alignment of all the landmark maps between all the studied gels, and also on the DP stained proteomic map (i.e. HSP71 in B1) is the first step of analysis. Applied to the analysis of the reactivity of the 2 sera from patients with autoimmune diseases, this procedure demonstrated the co-alignment of antigenic, anchor and proteomic spots identified as ENOA by MS/MS (blue circles in B2), thus confirming that these patients had anti-ENOA autoantibodies. Using this procedure to analyze the anti-G3P (blue circles in B3) reactivity of the same 2 sera, we confirmed the data of SERPA for serum 2, which had anti-G3P autoantibodies. For serum 1, whereas SERPA had suggested a strong reactivity against G3P, FBIP approach revealed a weak reactivity against this target (blue circles in B3), but strong reactivity against smaller protein targets neighboring the G3P (red circles in B3), highlighting a clear mismatch of the SERPA procedure. Additional samples analyzed with the same procedures demonstrate the robustness of the FBIP approach (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132142#pone.0132142.s004" target="_blank">S3 Fig</a>).</p