The promising future of proteomics in sarcoidosis.

Proteomic technologies are widely used to identify biomarkers for the early detection of human diseases, to develop predictive models of classification, and for monitoring the therapeutic efficacy of drugs. In this issue of the AJRCCM (pp. 1145–1154), Kriegova and colleagues (1) used an innovative proteomic technique, surface-enhanced laser desorption ionization–time-offlight mass spectrometry (SELDI-TOF MS) to examine patterns of protein expression in sarcoidosis. Mass spectrometry–based techniques may be considered a direct derivation of the original studies on proteomics by Hutchens and Yip (2). Combining chromatography and mass spectrometry, this platform is capable of detecting tens of thousands of data points in a short time from very small volumes (microliters) of biofluids containing a complex mixture of peptides or proteins, such as urine, serum, plasma, or bronchoalveolar lavage (BAL). The methodology resolves proteins, present in mixtures even at extremely low concentrations (femtoto attomoles), through a high-throughput approach (300 samples/day in batches of 100) (3). The principle behind the technique is very simple (Figure 1), with proteins of interest, such as those contained in the BAL, captured on an immobilized stationary-phase chip in an array format. The chip is then inserted into a vacuum chamber and bound proteins are irradiated with a laser that results in the molecules liberating gaseous ions. The ions are rapidly accelerated into a “flight tube” and the time of flight, which is related to the mass-to-charge ratio (m/z) of each protein/peptide, allows for their separation. An ion trap analyzer functions as a detector, which, when capturing the ions, starts to oscillate and transforms ion cyclotron resonance into signals. Detected proteins and peptides are then shown as a series of corresponding peaks. Since a typical mass spectrometry platform may generate a proteomic profile of up to 400,000 data points, sophisticated software packages are needed for the statistical analysis of large numbers of samples. The on-chip capture and detection of proteins have evident advantages; it allows small sample sizes and limited sample manipulation, and produces high-throughput results (3, 4). Taking advantage of these advances, mass spectrometry platforms have been used for the discovery of biomarkers in a large variety of diseases, including cancer and autoimmune disorders, as well as in neurologic and metabolic disorders (3). The tool is also beginning to be used in respiratory medicine. Zhukov and colleagues (5) utilized SELDI-TOF MS to generate specific protein peak patterns for malignant lung tumors, whereas Merkel and colleagues identified specific protein patterns in BAL fluid samples of patients with chronic obstructive pulmonary disease (6). The article published in this issue of the Journal represents an example of the potential utility of SELDI-TOF MS. The authors used this technique to examine the BAL proteome in patients with sarcoidosis. Data analysis identified a panel of 40 proteins that were altered in samples with this disorder versus those from healthy controls. Distinct protein patterns specific for patients with pulmonary sarcoidosis were identified and, more specifically, profiles were characterized from patients with sarcoidosis and Löfgren’s syndrome. The authors also found distin-