Raw file	Experiment	Enzyme	Enzyme mode	Enzyme first search	Enzyme mode first search	Use enzyme first search	Variable modifications	Multi modifications	Variable modifications first search	Use variable modifications first search	Requantify	Multiplicity	Max. missed cleavages	Labels0	LC-MS run type	Time-dependent recalibration	MS	MS/MS	MS3	MS/MS Submitted	MS/MS Submitted (SIL)	MS/MS Submitted (ISO)	MS/MS Submitted (PEAK)	MS/MS Identified	MS/MS Identified (SIL)	MS/MS Identified (ISO)	MS/MS Identified (PEAK)	MS/MS Identified [%]	MS/MS Identified (SIL) [%]	MS/MS Identified (ISO) [%]	MS/MS Identified (PEAK) [%]	Peptide Sequences Identified	Peaks	Peaks Sequenced	Peaks Sequenced [%]	Peaks Repeatedly Sequenced	Peaks Repeatedly Sequenced [%]	Isotope Patterns	Isotope Patterns Sequenced	Isotope Patterns Sequenced (z>1)	Isotope Patterns Sequenced [%]	Isotope Patterns Sequenced (z>1) [%]	Isotope Patterns Repeatedly Sequenced	Isotope Patterns Repeatedly Sequenced [%]	Recalibrated	Av. Absolute Mass Deviation [ppm]	Mass Standard Deviation [ppm]	Av. Absolute Mass Deviation [mDa]	Mass Standard Deviation [mDa]	Label free norm param
20170605_QEp3_OzKa_HA_CLIP_2	Flag_1	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)			False	True	1	2		Standard		15204	80249	0	96024	64454	0	31570	21544	20866	0	678	22.44	32.37	NaN	2.15	16407	1006914	73359	7.29	2118	2.89	145060	58926	57965	40.62	46.29	4689	7.96	+	0.54681	0.80666	0.34886	0.54179	
20170605_QEp3_OzKa_HA_CLIP_3	Flag_2	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)			False	True	1	2		Standard		14696	82474	0	97759	67173	0	30586	26968	25914	0	1054	27.59	38.58	NaN	3.45	20054	1024953	75557	7.37	2238	2.96	154449	61636	60681	39.91	44.98	4673	7.58	+	0.5631	0.83211	0.36029	0.55646	
20170605_QEp3_OzKa_HA_CLIP_4	Flag_3	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)			False	True	1	2		Standard		14796	82187	0	97323	67039	0	30284	25641	24642	0	999	26.35	36.76	NaN	3.3	18899	1012774	75393	7.44	2219	2.94	152885	61266	60244	40.07	44.97	4786	7.81	+	0.5569	0.82783	0.35896	0.55954	
20170605_QEp3_OzKa_HA_CLIP_6_170606150224	FlagUBL3_1	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)			False	True	1	2		Standard		14236	84293	0	98747	69831	0	28916	29622	28548	0	1074	30	40.88	NaN	3.71	23697	1066967	78367	7.34	1850	2.36	166856	65087	64100	39.01	44.13	4046	6.22	+	0.5899	0.8668	0.37679	0.57977	
20170605_QEp3_OzKa_HA_CLIP_7	FlagUBL3_2	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)			False	True	1	2		Standard		14304	83894	0	98517	69263	0	29254	29436	28361	0	1075	29.88	40.95	NaN	3.67	23542	1052524	77850	7.4	1792	2.3	163407	64429	63475	39.43	44.55	4078	6.33	+	0.58572	0.86434	0.37326	0.57381	
20170605_QEp3_OzKa_HA_CLIP_8	FlagUBL3_3	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)			False	True	1	2		Standard		14442	82945	0	98264	67602	0	30662	26850	25899	0	951	27.32	38.31	NaN	3.1	21704	1062129	76638	7.22	1906	2.49	159740	62743	61666	39.28	44.73	4091	6.52	+	0.5889	0.86423	0.37304	0.57131	
20170605_QEp3_OzKa_HA_CLIP_11	FlagUBL3CC_1	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)			False	True	1	2		Standard		18145	67722	0	87161	48217	0	38944	7452	7241	0	211	8.55	15.02	NaN	0.54	5927	985837	59619	6.05	1993	3.34	113833	43292	42269	38.03	45.79	3951	9.13	+	0.59218	0.83092	0.38204	0.56669	
20170605_QEp3_OzKa_HA_CLIP_12	FlagUBL3CC_2	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)			False	True	1	2		Standard		17466	70624	0	90450	50724	0	39726	9175	8878	0	297	10.14	17.5	NaN	0.75	7328	998098	62400	6.25	2164	3.47	119882	45619	44675	38.05	45.58	4093	8.97	+	0.57737	0.81748	0.36706	0.54798	
20170605_QEp3_OzKa_HA_CLIP_13	FlagUBL3CC_3	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)			False	True	1	2		Standard		17346	71066	0	90807	51249	0	39558	10485	10103	0	382	11.55	19.71	NaN	0.97	8266	1015574	62700	6.17	2214	3.53	121578	45967	44980	37.81	45.08	4147	9.02	+	0.5766	0.82445	0.36753	0.55437	
Flag_1																																16407																		
Flag_2																																20054																		
Flag_3																																18899																		
FlagUBL3_1																																23697																		
FlagUBL3_2																																23542																		
FlagUBL3_3																																21704																		
FlagUBL3CC_1																																5927																		
FlagUBL3CC_2																																7328																		
FlagUBL3CC_3																																8266																		
Total																	140635	705454	0	855052	555552	0	299500	187173	180452	0	6721	21.89	32.48	NaN	2.24	38091	9225770					1297690	508965	500055	39.22	45.06	38554	7.57		0.57461	0.84319	0.36694	0.56391