Two patterns of protein expression kinetics (from left to right): p209 cl1 (pure clone) shows the strongests spot, Mn cl2 (pure clone) shows the weakest spot; then: mixtures at different times of experiment.

<p>(a) Top row: the mixture at the end of the experiment exhibits overexpression by comparison with p209 cl1. (b) bottom row: the mixture at the end of the experiment shows underexpression by comparison with p209 cl1.</p

Bidimensionnal electrophoresis of the proteomic variability of the 2 <i>Trypanosoma cruzi</i> stocks P209 cl1 and Mn Cl2.

<p>The picture shows a total of 1,850 spots identified by Samespot. Circled and numbered spots correspond to the spots of interest identified by mass spectrometry. Above: PH gradient.</p

List of the proteins identified by mass spectrometry, their function and their pattern of behavior (over- vs. under-expressed) in the experiment.

<p>The Swissprot_TrEMBL entry is related to the reference of the protein in the Swissprot_TrEMBL database.</p><p>Score is calculated by the Mascot search engine for each identified protein matched from the MS peak list. If the Protein Score is equal to, or greater than, the Mascot Significance Level, the protein match is considered to be statistically non-random at the 95% confidence interval.</p

Differential expression of the salivary proteins between the susceptible Kis and resistant AceRKis SGE extracts.

<p>Differences in protein expression are represented as a function of both expression ratio (resistant/susceptible) and significance ratio (q-value). Vertical dotted lines indicate the 1.5-fold difference in expression level in either direction (x1.5 for a higher expression in the resistant strain and/1.5 for a lower expression in the resistant strain). The horizontal dotted line indicates a q-value  = 0.05 (or 1/q  = 20). Saglin and TRIO proteins display expression level differences above 3 and highly significant q-values.</p

Differentially expressed salivary gland proteins between the susceptible Kis and resistant AceRKis strains.

<p>Protein identification was performed using MALDI-TOF MS or nanoLC ESI MS/MS (underlined spot#) analysis. Insecta entries of Swiss-Prot and TrEMBL databases were searched by using the MASCOT algorithm, or the Proteome Discoverer software for nanoLC ESI MS/MS spectra. All spots displayed a power >0.9. Spot# refers to the SameSpots analysis spot number (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103816#pone-0103816-g001" target="_blank">Figure 1A</a>); ^SP indicates the presence of a signal peptide for secretion as predicted by SignalP 4.0 (<i>^SP°</i>: SP in the N-terminal homolog Q5TV62_ANOGA); Fold: fold difference in expression levels between the two strains; Accession: accession number in UniProtKB/Swiss-Prot or UniProtKB/TrEMBL databases (_ANOGA); pI: isoelectric point; Cover: indicates the amino acid coverage (%); *Mascot Score is provided for MALDI-TOF protein identification; for nanoLC ESI MS/MS based identification the peptide sequences and the number of peptides are provided as supporting information (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103816#pone.0103816.s001" target="_blank">Table S1</a>). Translation IF: Translation Initiation Factor.</p

Workflow to decipher the molecular cross-talk between human cells and the obligate intracellular parasite <i>A. algerae</i> which is characterized by a strong host dependency.

<p>HFF cells labelled with ¹³C₆¹⁵N₂-lysine (dark gray) were submitted to either infection by <i>A. algerae</i> or hypoxic stress. For each time point of both kinetics the labeled cells were combined at 1∶1 ratio with unlabeled HFF cells (light gray) and proteins were extracted. For each sample a three biological replicate was made. The proteins samples were resolved on SDS-PAGE and total proteins lanes were cut in 3 regular pieces (A, B, C) and processed for in-gel digestion with endoproteinase LysC. LC-MS/MS analysis was then performed and mass spectra were analyzed with the MaxQuant software to achieve the relative protein quantification.</p

Clusters of the host proteins significantly modulated during the hypoxia treatment.

<p>HFF cells at confluence were submitted to an abiotic stress (i.e. hypoxic) at two different cell ages 24 hours (H24) and 8 days (D8). Proteins expression levels were clustered by using methods described here before in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0100791#pone.0100791.s001" target="_blank">Fig S1</a>.</p

Clusters of the host proteins significantly modulated during the kinetics of infection.

<p>HFF cells at confluence were infected by 1×106 spores of A. algerae and samples were taken 1 hour post infection (H1), 6 hour post infection (H6), 12 hour post infection (H12), 24 hour post infection (H24) and 8 day post infection (D8). Log2 Protein ratio were measured using the SILAC workflow and were relative to the uninfected cells. Genes were selected for this analysis if their expression level differed significantly from the control for at least one time point. The color scale ranges from saturated green for log ratios −3.15 and below to saturated red for log ratios 3.15 and above. Each gene is represented by a single row of colored boxes and each time point is represented by a single column.</p