Table 1.

List of different matrices investigated and of methods applied for the proteomic profiling of pulmonary diseases considered in this report. iTRAQ, isobaric tags for relative and absolute quantitation; 1DE, one-dimensional gel electrophoresis; NSCLC, non-small cell lung cancer; BALf, bronchoalveolar lavage fluid.

Method	Matrix	Reference
Cancer
iTRAQ-2D-LC-MS/MS	A549 human lung carcinoma cell line	[25]
Isoelectric focusing (IEF);	Human H69 and H69AR small lung cancer cell line	[26]
iTRAQ-1D-LC-MS/MS	H358 human non-small cell lung adenocarcinoma cell line	[27]
1DE; iTRAQ-1D-LC-MS/MS	CL1-0 and CL1-5 lung cancer cell lines	[28]
iTRAQ-1D-LC-MS/MS	HCC827 and PC9 cell lines	[29]
1DE; 1D-LC-MS/MS	NSCLC cell lines	[45]
	A549 human lung carcinoma cell line	[49]
1D-LC-MS/MS	NSCLC cell lines	[46]
	CL1-0 and CL1-5 lung cancer cell lines	[47]
	A549 human lung carcinoma cell line	[48,50,59]
	H23, H520, H460 and H1688 cell lines	[56]
1DE; 2D-LC-MS/MS	NSCLC cell lines	[52]
2DE; 2D-LC-MS/MS	NCI-H125 NSCLC cell line	[54]
2D-LC-MS/MS	QU-DB and Mehr 80 LCC cell lines	[58]
1D-LC-MS/MS	Human plasma	[60]
2D-LC-MS/MS		[61,62]
2D-LC-MS/MS	Human serum	[61]
1D-LC-MS/MS		[62,63,64,65,66,68]
1DE; 1D-LC-MS/MS		[67]
2DE; 1D-LC-MS/MS	Human lung tumor tissues	[70,77]
1D-LC-MS/MS		[71,72]
iTRAQ-1D-LC-MS/MS		[73]
2D-LC-MS/MS		[74]
iTRAQ-2D-LC-MS/MS		[75]
IEF-1D-LC-MS/MS		[76]
2D-LC-MS/MS	Lung adenocarcinoma pleural effusions	[78]
1D-LC-MS/MS		[79]
1DE; 1D-LC-MS/MS	Human urine	[80]
Asthma
iTRAQ-MS/MS; LC-MRM/MS	Human plasma	[81]
1D-LC-MS/MS	Induced sputum	[82]
1D-LC-MS/MS	Exhaled breath condensate	[6]
1DE; 1D-LC-MS/MS	BALf	[88]
Cystic fibrosis
2DE-MS/MS; 1DE-LC-MS/MS	IB3-1 And IB3-1/S9 cell lines	[89]
2DE; 1D-LC-MS/MS	Human serum	[90]
COPD
CapLC-MS/MS	Induced sputum	[3]
1D-LC-MS/MS	Exhaled breath condensate	[8]
1D-LC-MS/MS	BALf	[93]
“Minor” respiratory diseases
1DE; 1D-LC-MS/MS	Human lung tissue	[94]
Size exclusion chromatography (SEC); 1D-LC-MS/MS	BALf	[95]