Around 1300 protein spots were detected on each 2D-DIGE gels in DeCyder 2D software analysis. In 2D-DIGE analysis of FM and HC, total of 121 (around 9.3% of the entire detected spots) differentially expressed spots satisfied the statistical parameters (t-test; p,0.05), among which, 70 protein spots were up-regulated (with changes from 1.02 to 50.9-fold) and the remaining 51 were down-regulated (range from 1.2 to 24-fold) (Table S1 .2). Out of 121 spots, 36 and 9 spots were found to be statistically significant after performing false discovery rate (FDR) correction (Benjamini-Hochberg) and Bonferroni correction, respectively (Table S1 .2). All of the 121 differentially expressed spots (in FM compared to HC) identified in 2D-DIGE analysis were excised and subjected to MALDI-TOF/TOF MS analysis. We obtained reliable MS IDs for 63 protein spots out of 121 (Table S2. 2); while remaining 58 spots remained unidentified and produced virtually empty spectra, most likely owing to the presence of extremely diminutive quantity of proteins as indicated by the retrospective scrutiny of the spot volumes. The 63 protein spots identified by MS represented 30 (14 up-regulated and 16 down-regulated) differentially expressed proteins in FM patients ( Table 2 ; Figure 1C and S3). Proteins identified in 2DE experiment were also obtained in 2D-DIGE; additionally, new candidates were also identified by 2D-DIGE due to the higher sensitivity and reproducibility. 3D views and graphical representation of selected protein spots are shown in Figure 1D .