International Journal of Proteomics

Research Article

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

Table 3

Summary of LC-ESI-MS/MS data when considering urea denaturation as a 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.
ExtractionControlQkit(A)(B)(C)(D)(E)(F)
Detected spectra6333767411462796488959074492136893248689
Detected proteins125211419051236120885211811060
Median percent sequence coverage11.415.215.511.910.616.010.910.7
Percent sequence coverage interquartile range15.921.121.017.514.823.716.315.7
Detected peptides902596287596100558431773191257862
Mean peptide length15 ± 613 ± 514 ± 515 ± 615 ± 614 ± 515 ± 616 ± 6
K-terminal peptides244439429119662092739513369
R-terminal peptides86244986453089368074487584747343
Peptide K : R0.0280.8810.6430.1080.0260.5620.0610.050
Carbamyl N-terminus2831276200200136180194
Carbamyl lysine372228938663466112734273009
Total carbamyl groups54383017052684821136847274196
Percent total carbamylation60.30.022.252.457.217.751.853.4
Total missed cleavages67951004274768355950299464856367
Missed lysine cleavages5705781200059085106243852654717
Missed arginine cleavages109022374792784455612201650
Percent missed cleavages out of total peptides75.38.136.168.070.638.771.181.0