International Journal of Proteomics

Research Article

Optimization of Urea Based Protein Extraction from Formalin-Fixed Paraffin-Embedded Tissue for Shotgun Proteomics

Table 2

Summary of LC-ESI-MS/MS data without considering urea denaturation as special factor in ProteinPilot. Detected peptides were limited to 1% global FDR. Detected proteins were limited to 2 peptides and 1% global FDR. Percent total carbamyl lysine was calculated as the number of total carbamyl groups out of the total number of peptides. Percent missed cleavages were calculated as the total number of missed cleavages out of the total number of peptides.


	Control	Qkit	(A)	(B)	(C)	(D)	(E)	(F)

Detected spectra	43657	67411	45073	49333	40871	45571	52207	35281
Detected proteins	948	1141	891	1027	888	835	957	836
Detected peptides	6318	9628	7104	7780	5868	7292	7153	6132
K-terminal peptides	180	4394	2725	734	124	2552	411	301
R-terminal peptides	6030	4986	4234	6936	5646	4627	6638	5718
Peptide K : R	0.03	0.881	0.644	0.106	0.022	0.552	0.05	0.053
Carbamyl N-terminus	506	12	36	564	451	241	468	420
Carbamyl lysine	1211	2	33	1467	1066	428	1120	959
Total carbamyl groups	1749	30	72	2057	1535	681	1612	1407
Percent total carbamylation	27.7	0.3	1.0	26.4	26.2	9.3	22.5	22.9
Total missed cleavages	3052	1004	2493	3728	2656	2517	3749	3833
Missed lysine cleavages	2322	781	1811	3021	2077	1984	2796	2529
Missed arginine cleavages	730	223	682	707	579	533	953	1304
Percent missed cleavages out of total peptides	48.3	10.4	35.1	47.9	45.3	34.5	52.4	62.5