uPU-60mingradTOP20-highload_Luciano_IP_gradient_45min_3_to_50_375_1500
Description: 1h method suitable for DDA LFQ analysis of relatively lower complexity samples like IPs Flow rate: 0.3 µL/min LC gradient: 3 % B over 3 minutes; 3 to 50 % B over 45 minutes; 50 to 80 % B over 2 minutes; then wash at 80 % B over 5 minutes, 80 to 3 % B over 2 minutes and then the column was equilibrated with 3 % B for 3 minutes Top N: 25 Resolution MS1: 120000 m/z range: 375-1500 Charge states: 2-6 Fragmentation: HCD @ 30% Resolution MS2: 15000 Max. inj. Time: 50 ms
uPU-90mingradTOP20-highload_Luciano_375_1500
Description: 2h method suitable for DDA LFQ analysis of complex samples (e.g. Whole cell lysates, Lyso IPs) Flow rate: 0.3 µL/min LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 87 minutes; 45 to 80 % B over 1 minute; then wash at 80 % B over 14 minutes, 80 to 3 % B over 1 minutes and then the column was equilibrated with 3 % B for 14 minutes Top N: 25 Resolution MS1: 120000 m/z range: 375-1500 Charge states: 2-6 Fragmentation: HCD @ 30% Resolution MS2: 15000 Max. inj. Time: 50 ms
uPU-60mingradTOP20-highload_Luciano_IP_gradient_375_1500
Description: 1h method suitable for DDA LFQ analysis of relatively lower complexity samples like IPs Flow rate: 0.3 µL/min LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 25 minutes; 45 to 80 % B over 14 minutes; then wash at 80 % B over 5 minutes, 80 to 3 % B over 3 minutes and then the column was equilibrated with 3 % B for 10 minutes Top N: 25 Resolution MS1: 120000 m/z range: 375-1500 Charge states: 2-6 Fragmentation: HCD @ 30% Resolution MS2: 15000 Max. inj. Time: 50 ms
uPU-90mingradTOP25-TMT-5microscan-375_1500 and uPU-90mingradTOP25-TMT-1microscan-375_1500
Description: 2h method suitable for analysis of TMT labeled complex samples (e.g. Whole cell lysates, Lyso IPs) Flow rate: 0.3 µL/min LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 87 minutes; 45 to 80 % B over 5 minutes; then wash at 80 % B over 6 minutes, 80 to 3 % B over 5 minutes and then the column was equilibrated with 3 % B for 14 minutes Top N: 25 Resolution MS1: 120000 m/z range: 375-1500 Isolation Window: 0.7 (vs 1.4) Charge states: 2-6 Fragmentation: HCD @ 36% Resolution MS2: 45000 Max. inj. Time: 105
uPU-90mingradTOP20-highload_Luciano
Description: 2h method suitable for DDA LFQ analysis of complex samples (e.g. Whole cell lysates, Lyso IPs) Flow rate: 0.3 µL/min LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 87 minutes; 45 to 80 % B over 1 minute; then wash at 80 % B over 14 minutes, 80 to 3 % B over 1 minutes and then the column was equilibrated with 3 % B for 14 minutes Top N: 25 Resolution MS1: 120000 m/z range: 200-2000 Charge states: 2-6 Fragmentation: HCD @ 30% Resolution MS2: 15000 Max. inj. Time: 50 ms
uPU-60mingradTOP20-highload_Luciano_IP_gradient
Description: 1h method suitable for DDA LFQ analysis of relatively lower complexity samples like IPs Flow rate: 0.3 µL/min LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 25 minutes; 45 to 80 % B over 14 minutes; then wash at 80 % B over 5 minutes, 80 to 3 % B over 3 minutes and then the column was equilibrated with 3 % B for 10 minutes Top N: 25 Resolution MS1: 120000 m/z range: 200-2000 Charge states: 2-6 Fragmentation: HCD @ 30% Resolution MS2: 15000 Max. inj. Time: 50 ms
uPU-60mingradTOP20-highload_Luciano_IP_gradient_charges4-8
Description: 1h method suitable for DDA LFQ analysis of relatively lower complexity and high charge like cross-linked IPs Flow rate: 0.3 µL/min LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 25 minutes; 45 to 80 % B over 14 minutes; then wash at 80 % B over 5 minutes, 80 to 3 % B over 3 minutes and then the column was equilibrated with 3 % B for 10 minutes Top N: 25 Resolution MS1: 120000 m/z range: 200-2000 Charge states: 4-8 Fragmentation: HCD @ 30% Resolution MS2: 15000 Max. inj. Time: 50 ms
uPU-90mingradTOP20-highload_Luciano_IP_gradient_375_1500_ORF1_exclusion
Description: 2h method suitable for DDA LFQ analysis with an exclusion list for all ORF1 peptides Flow rate: 0.3 µL/min LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 87 minutes; 45 to 80 % B over 1 minute; then wash at 80 % B over 14 minutes, 80 to 3 % B over 1 minutes and then the column was equilibrated with 3 % B for 14 minutes Top N: 30 Resolution MS1: 120000 m/z range: 375-1500 Charge states: 2-5 Fragmentation: HCD @ 30% Resolution MS2: 15000 Max. inj. Time: 50 ms
uPU-90mingradTOP20-highload_Luciano_IP_gradient_375_1500_ORF2_inclusion
Description: 2h method suitable for DDA LFQ analysis with an inclusion list for all ORF2 peptides Flow rate: 0.3 µL/min LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 87 minutes; 45 to 80 % B over 1 minute; then wash at 80 % B over 14 minutes, 80 to 3 % B over 1 minutes and then the column was equilibrated with 3 % B for 14 minutes Top N: 30 Resolution MS1: 120000 m/z range: 375-1500 Charge states: 2-5 Fragmentation: HCD @ 30% Resolution MS2: 15000 Max. inj. Time: 50 ms
uPU-90mingradTOP20-highload_Luciano_IP_gradient_375_1500_ORF2_inclusion_ORF1_exclusion
Description: 2h method suitable for DDA LFQ analysis with an inclusion list for all ORF2 peptides AND an exclusion list for all ORF1 peptides Flow rate: 0.3 µL/min LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 87 minutes; 45 to 80 % B over 1 minute; then wash at 80 % B over 14 minutes, 80 to 3 % B over 1 minutes and then the column was equilibrated with 3 % B for 14 minutes Top N: 30 Resolution MS1: 120000 m/z range: 375-1500 Charge states: 2-5 Fragmentation: HCD @ 30% Resolution MS2: 15000 Max. inj. Time: 50 ms
uPU-90mingradTOP25-LFQ-1microscan-375_1500
Description: 2h method suitable for DDA LFQ analysis of complex samples (e.g. Whole cell lysates, Lyso IPs) Flow rate: 0.3 µL/min LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 87 minutes; 45 to 80 % B over 5 minute; then wash at 80 % B over 6 minutes, 80 to 3 % B over 5 minutes and then the column was equilibrated with 3 % B for 14 minutes Top N: 25 Resolution MS1: 120000 m/z range: 375-1500 Charge states: 2-5 Fragmentation: HCD @ 30% Resolution MS2: 15000 Max. inj. Time: auto
uPU-90mingrad_Hload_DIA_375_1500_window_15
Description: 2h method suitable for DIA analysis of complex samples (e.g. Whole cell lysates, Lyso IPs) Flow rate: 0.3 µL/min LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 87 minutes; 45 to 80 % B over 5 minutes; then wash at 80 % B over 6 minutes, 80 to 3 % B over 5 minutes and then the column was equilibrated with 3 % B for 14 minutes Isolation Window: 15 Resolution MS1: 120000 m/z range: 375-1500 Fragmentation: HCD @ 32% Resolution MS2: 30000 Max. inj. Time: Auto
uPU-60mingrad_Hload_DIA_375_1500_window_15
Description: 1h method suitable for DIA analysis of relatively lower complexity samples like IPs LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 25 minutes; 45 to 80 % B over 14 minutes; then wash at 80 % B over 5 minutes, 80 to 3 % B over 3 minutes and then the column was equilibrated with 3 % B for 10 minutes Isolation Window: 15 Resolution MS1: 120000 m/z range: 375-1500 Fragmentation: HCD @ 32% Resolution MS2: 30000 Max. inj. Time: Auto
uPU-60mingrad_Hload_DIA_300_1500_window_15
Description: 1h method suitable for DIA analysis of relatively lower complexity samples like IPs LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 25 minutes; 45 to 80 % B over 14 minutes; then wash at 80 % B over 5 minutes, 80 to 3 % B over 3 minutes and then the column was equilibrated with 3 % B for 10 minutes Isolation Window: 15 Resolution MS1: 120000 m/z range: 300-1500 Fragmentation: HCD @ 32% Resolution MS2: 30000 Max. inj. Time: Auto
uPU-60mingradTOP25-TMT-1microscan-200_2000
Description: 1h method suitable for analysis of TMT labeled samples with relatively low complexity like IPs Flow rate: 0.3 µL/min LC gradient: 3 % B over 3 minutes; 3 to 45 % B over 25 minutes; 45 to 80 % B over 14 minutes; then wash at 80 % B over 5 minutes, 80 to 3 % B over 3 minutes and then the column was equilibrated with 3 % B for 10 minutes Top N: 25 Resolution MS1: 120000 m/z range: 200-2000 Isolation Window: 1.4 Charge states: 2-6 Fragmentation: HCD @ 36% Resolution MS2: 45000 Max. inj. Time: 50