Skyline output and calibration range for GHTVDSELTTEDPVIQKK.

<p>Retention time is displayed on x axis and intensity for each ion or fragment is displayed on y axis. Each parent ion and fragment is shown in a different colour. AUC corresponds to the integration of signal under the curve (A). Regression line is obtained using AUC from each concentration point.</p

Geographic origin of the samples used for genomic studies of <i>PFI1785w</i>.

<p>Geographic origin of the samples used for genomic studies of <i>PFI1785w</i>.</p

Linear regression line obtained with Skyline integration of raw files.

<p>Linear regression line obtained with Skyline integration of raw files.</p

Secondary structure of PFI1785w predicted using Phyre 2 and predictive 3D structure of amino-acid 224–360.

<p>Secondary structure of PFI1785w predicted using Phyre 2 and predictive 3D structure of amino-acid 224–360.</p

Peptide concentration measured within calibration range of each peptide.

<p>Peptide concentrations calculated by linear regression for each studied protein, y axis presents peptide concentration. Each dot represents one sample, and reference strains are displayed separately on the right of each plot (CSA+: CSA adhesion selected parasite strain, CSA-: non selected parasite strain). PAM samples and CSA+ parasite strains display a placental malaria like binding phenotype (in red), and UM samples and CSA- parasite strain display a uncomplicated malaria phenotype (in blue). PF14_0018, PFA_0410w, PFB0115w and PFI1785w are preferentially found in PAM like samples.</p

Transitions used in SRM experiments for peptides WQQGNIFSCSVMHEALHNR (#24, G3m5*) and WQEGNVFSCSVMHEALHNR (#26, G3m24*).

<p>3+: The precursor ions were in triply-charged form; m/z: mass to charge ratio; ox: oxidized methionine (M), accepted nomenclature for fragment ions as proposed by Roepstorff and Fohlman <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Roepstorff1" target="_blank">[25]</a>; bolded are the heavy arginine.</p

Mass-to-charge ratios (m/z) of thirty-two G3m and IGHG3 allele peptides after AspN and trypsin digestion.

<p>The proteotypic peptides correspond to an enzymatic AspN and trypsin digestion of the constant region of the IG gamma3 chains encoded by the <i>Homo sapiens</i> IGHG3 gene. Masses are determined for detection on the MALDI TOF and ESI Orbitrap mass spectrometers. The methionine (M) could be oxidized (+16 Da). m/z : mass-to-charge ratio; +1, +2, +3, +4 represent the peptide charge state; amino acids in bold are implicated in the discrimination between G3m and IGHG3 alleles (detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone-0046097-t002" target="_blank">Table 2</a>); «.» : site of enzymatic cut; C^c : carbamidomethylated cysteine.</p

Characteristics of the thirty-two proteotypic peptides for <i>Homo sapiens</i> G3m and IGHG3 alleles.

<p>The proteotypic peptides correspond to an enzymatic AspN and trypsin digestion of the constant region of the IG gamma3 chains encoded by the <i>Homo sapiens</i> IGHG3 gene.</p>a<p>Partial.</p>b<p>Unusual G3m allele <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Lefranc3" target="_blank">[8]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Dard1" target="_blank">[12]</a>. This corresponds to the IGHG3*08 allele. Allotypes G3m10, G3m11 and G3m13 are not expressed owing to the presence of CH3 Asn N44, instead of the CH3 Ser S44 usually present in the other G3m5* alleles <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Lefranc3" target="_blank">[8]</a>.</p>c<p>The IGHG3*11 and IGHG3*12 alleles differ by the number of hinge exons, 4 and 3, respectively (IMGT Repertoire, Gene table <a href="http://www.imgt.org" target="_blank">http://www.imgt.org</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Lefranc3" target="_blank">[8]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Giudicelli1" target="_blank">[18]</a>.</p>d<p>Expression of the allotype G3m15 is dependent, in addition to CH3 Met M39, on the presence of CH3 His H115 and Tyr Y116 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Lefranc3" target="_blank">[8]</a>.</p>e<p>Expression of the allotype G3m13 is dependent, in addition to CH3 Gln Q98, on the presence of CH3 Ser 44 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Lefranc3" target="_blank">[8]</a>.</p>f<p>Expression of the allotype G3m10 is dependent, in addition to CH3 Ile I101, on the presence of CH3 Ser 44 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Lefranc3" target="_blank">[8]</a>.</p>g<p>Expression of the allotype G3m15 is dependent, in addition to CH3 His H115 and Tyr Y116, on the presence of CH3 Met M39 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Lefranc3" target="_blank">[8]</a>.</p>h<p>Expression of the allotype G3m14 is dependent, in addition to CH3 Arg R115 and Phe F116, on the presence of CH3 Met M84 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Lefranc3" target="_blank">[8]</a>.</p>i<p>Expression of the allotype G3m6 is dependent, in addition to CH3 Glu E98, on the presence of CH3 Ser S44 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Lefranc3" target="_blank">[8]</a>.</p>j<p>Expression of the allotype G3m24 is dependent, in addition to CH3 Val V101, on the presence of CH3 Ser S44 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Lefranc3" target="_blank">[8]</a>.</p><p>Amino acids in bold are implicated in the discrimination between IGHG3 alleles. “.” : site of enzymatic cut.</p><p>Amino acids characteristic of the G3m allotypes and IGHG3 alleles are from reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Lefranc3" target="_blank">[8]</a>. They are illustrated in the ‘IMGT G3m allele butterfly’ representation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Lefranc3" target="_blank">[8]</a>. Amino acid sequences are available in the IMGT Repertoire (<a href="http://www.imgt.org" target="_blank">http://www.imgt.org</a>), IMGT/DomainDisplay and IMGT/GENE-DB <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Giudicelli1" target="_blank">[18]</a>. Positions in the CH domains are according to the IMGT unique numbering for C domain <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046097#pone.0046097-Lefranc6" target="_blank">[21]</a>.</p

Relative abundance of a volume/volume mixture from BEC1 (G3m5*) and BEC2 (G3m5*/G3m24*) plasma samples.

<p>The relative abundance was calculated by the Progenesis LC-MS software for label-free semi-quantitative data analysis (detailed in 2.7); +2: dicharged peptides; the light grey bars represent the measure of the WQ<b>E</b>GN<b>V</b>FSCVMHEALHNR (#26, G3m24*) peptide (only brought by BEC2), the dark grey bars taken all together represent the measure of the WQ<b>Q</b>GN<b>I</b>FSCVMHEALHNR (#24, G3m5*) peptide (brought by both BEC1 and BEC2). The dark grey bars were divided into a hatched part (for the deduced signal attributable to BEC2, calculated from the 0∶1 ratio) and a non-hatched part (for the deduced signal attributable to BEC1).</p

Protein-A and Protein-G purification fractions from the EUA1 plasma sample on an acrylamid gel.

<p>A. 12% SDS-PAGE in non-reducing conditions: lines AF1 to AF3: consecutive filtrate fractions of a Protein A column containing plasma proteins including IgG3; line AE: Elution fraction of a Protein A column containing IgG1, IgG2, IgG4; lines GE1 and GE2: consecutive elution fractions of a Protein G column containing IgG3. B. 12% SDS-PAGE in reducing conditions: lines GE1 and GE2: consecutive elution fractions of a Protein G column containing IgG3.</p