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Background  The spirochete bacterium  Treponema pallidum  ssp.  pallidum  is the etiological agent of syphilis, a chronic multistage disease. Little is known about the global  T .  pallidum  proteome, therefore mass spectrometry studies are needed to bring insights into pathogenicity and protein expression profiles during infection.    Methodology/Principal Findings  To better understand the  T .  pallidum  proteome profile during infection, we studied  T .  pallidum  ssp.  pallidum  DAL-1 strain bacteria isolated from rabbits using complementary mass spectrometry techniques, including multidimensional peptide separation and protein identification via matrix-assisted laser desorption ionization-time of flight (MALDI-TOF/TOF) and electrospray ionization (ESI-LTQ-Orbitrap) tandem mass spectrometry. A total of 6033 peptides were detected, corresponding to 557 unique  T .  pallidum  proteins at a high level of confidence, representing 54% of the predicted proteome. A previous gel-based  T .  pallidum  MS proteome study detected 58 of these proteins. One hundred fourteen of the detected proteins were previously annotated as hypothetical or uncharacterized proteins; this is the first account of 106 of these proteins at the protein level. Detected proteins were characterized according to their predicted biological function and localization; half were allocated into a wide range of functional categories. Proteins annotated as potential membrane proteins and proteins with unclear functional annotations were subjected to an additional bioinformatics pipeline analysis to facilitate further characterization. A total of 116 potential membrane proteins were identified, of which 16 have evidence supporting outer membrane localization. We found 8/12 proteins related to the paralogous  tpr  gene family: TprB, TprC/D, TprE, TprG, TprH, TprI and TprJ. Protein abundance was semi-quantified using label-free spectral counting methods. A low correlation (r = 0.26) was found between previous microarray signal data and protein abundance.    Conclusions  This is the most comprehensive description of the global  T .  pallidum  proteome to date. These data provide valuable insights into  in vivo T .  pallidum  protein expression, paving the way for improved understanding of the pathogenicity of this enigmatic organism.

Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry