Application of Proteomics and Peptidomics to COPD

Table 1

Samples, MS methods, and major proteins/peptides (involved in COPD pathogenesis) detected.

Sample	Methods	Major proteins/peptides detected	Reference
Plasma	2D-PAGE^(a) MALDI-TOF	𝛼2-Macroglobulin, haptoglobin, ceruloplasmin, and hemopexin	[7]
Serum	Microarray	Interleukin-8 and matrix metalloproteinase-9	[8]
Serum	SELDI-TOF	Serum amyloid A	[9]
Plasma	High-resolution LC/FT-ICR MS^(b)	55 peptides mapped to 33 unique proteins, 12 of them with known roles in the complement or coagulation cascade	[10]
IS	2D-PAGE; GeLC-MS/MS^(c)	More than 250 proteins; Three members of the annexin; family, kallikreins 1 and 11, and peroxiredoxins 1, 2, and 5	[13]
IS	2-DE LC-MS/MS	Lipocalin and apolipoprotein A1	[14]
IS	2D-DIGE^(d) MALDI-TOF	Polymeric immunoglobulin receptor (PIGR)	[15]
IS	CapLC-MS/MS	203 proteins identified, Zn-𝛼2-glycoprotein, Clara cell, PRR4, LPLUNC2; 𝛽-actin, MUC5A/C, MUC5B, histone 4, lipocalin 1,; SPLUNC1, cathepsin G, Ig J, Ig 𝜇 heavy, and Ig 𝛾1	[16]
IS	SELDI-TOF	Calgranulins and Clara cell secretory protein	[17]
IS	MSB^(e)/MALDI-TOF	Antimicrobial peptides 𝛼-defensins	[18]
EBC	1-DE, 2-DE, 𝜇-HPLC and ESI-MS/MS, and SELDI-TOF	Cytokines (IFN-𝛾, IL-2, and IL-15); Cytokeratins (CK-1, CK-9, and CK-10)	[19]
EBC	LC-MS/MS and SELDI-TOF	Cytokines, type I and II, cytokeratins, two surfactant protein A isoforms, and calgranulins A and B	[20]
BALF	SELDI-TOF; RP-LC^(f); MALDI-TOF; LC-MS/MS	Lysozyme C, calgranulins A and B, and neutrophil defensins 1 and 2	[21]
BALF	2D-PAGE MALDI-TOF	200 proteins in the BAL proteome, proteins associated with redox reactions, immune reactivity, and inflammation	[22]
Lung tissue	2D-PAGE MALDI-TOF	Surfactant protein A	[23]
Lung tissue	2D-PAGE MALDI-TOF	Matrix metalloproteinase-13 (MMP-13) and thioredoxin-like 2	[24]
Lung tissue	2D-PAGE MALDI-TOF	Antioxidant enzymes, glucose-regulated protein 78, calreticulin, and S100A9/calgranulin C	[25]

IS: induced sputum. EBC: exhaled breath condensate. BALF: bronchoalveolar lavage fluid.
(a)2D-PAGE: two-dimensional polyacrylamide gel electrophoresis.
(b)FT-ICR MS: Fourier transform-ion cyclotron resonance.
(c)GeLC-MS/MS: proteins are separated by standard SDS-PAGE gel which is then cut into 25 pieces. Each gel slice is then cleaved by trypsin and then further fractionated by LC separation. Peptide fragments are then analysed by MS/MS.
(d)2D-DIGE: two-dimensional difference gel electrophoresis.
(e)MSBs: mesoporous silica beads.
(f)RP-LC: reverse-phase liquid chromatography.