Table 1.

Biospecimens for Proteomic Investigations in Sarcoidosis

	Advantages	Limitations	Sample-Specific Recommendation for Sarcoidosis	Role in Sarcoidosis
Lung/other tissue	Samples the site of injury Highest likelihood to capture biological changes	Granulomatous changes are patchy and prone to missed sampling Limited amount of tissue available Need invasive procedures for biopsy Contamination of tissue samples by blood and plasma proteins	Snap-freeze lung tissue promptly Washing before sample preparation for proteomics	Determine biological mechanism of granulomatous inflammation Promising for integration with other omics, including genomics
BALF	Easy to obtain via bronchoscopy Samples epithelial lining fluid (most proximate to the site of injury) Samples proteins from diverse cellular sources Used with standardized protocols by several investigators	High salt content needs removal (10) Variable dilution because of unpredictable volume of return High dynamic range because of albumin and other proteins Surfactant protein may impact spectral data acquisition	Enrichment of specific proteins of interest or removal of higher abundance proteins Standardized protocols for sample collection and storage Salt removal before analysis Avoid freeze-thaw	Better suited for developing biomarkers for diagnosis and prognosis Promising for integrative omics, such as metabolomics, but not genomics because of limited availability of RNA
BAL cells	Easy to obtain via bronchoscopy Identifies immune mechanisms by sampling inflammatory cells	Large volume lavage to ensure adequate cellular yield Contamination by red blood cells Variable proportion of cells depending on disease states and environmental exposures	Account for cell proportion during assay and analysis Cryopreservation may alter cellular proteins Avoid freeze-thaw	Determine biological mechanism of granulomatous inflammation Promising for integration with other omics, including genomics
EBC	Can be obtaining without any procedures Could be repeated without difficulty	Because EBC is >99% condensed water vapor (20), most analytes are close to the detection limit (10, 91) Variable collection methods alter EBC analytes and concentrations	Standard procedures to minimize the variability in collection (20)	Limited role unless standardized sample preparation and improved resolution of MS instruments
Sputum	Easy to obtain	Variable viscosity from sampling methods and sputum components Large amounts of mucins Contamination by oral microbes and microbial peptides	Adding reducing agents such as DTT (20), size-exclusion with or without dialysis (24), or gel-cleanup (92) to remove mucins Standardized approach to sample collection and processing Acetone precipitation for protein isolation	Unexplored but challenging for sarcoidosis pathogenesis and biomarker discovery
Blood-based proteomics	Easy to obtain without special procedures Better to capture systemic changes beyond organ-specific changes	High dynamic range of plasma Low-abundance proteins or those with a small change may be difficult to quantify reliably High-abundance protein removal techniques may remove other proteins Semple preparation could decrease throughput for discovery studies	Plasma is preferred over serum with EDTA (over heparin) (93) Removal of high-abundance proteins to improve depth of coverage (94) Fractionation before MS analysis (95) Removal of disease-relevant proteins bound to high-abundance proteins remains a challenge	Biomarker in blood would be idea for diagnosis and prognosis Targeted proteomics approaches offer promise to develop diagnostic tools and clinical assay

Definition of abbreviations: BALF = BAL fluid; EBC = exhaled breath condensate; MS = mass spectrometry.

The official report of the American Thoracic Society workgroup on metabolomics and proteomics offers guidance on techniques and challenges and recommendations for sample handling and processing (10).