Raw file	Experiment	Enzyme	Enzyme mode	Enzyme first search	Enzyme mode first search	Use enzyme first search	Variable modifications	Fixed 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
20190821_JH_EV_Ubi	821_JH_EV_Ubi	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term);GlyGly (K);Deamidation (NQ)	Carbamidomethyl (C)			False	True	1	2		Standard		4648	12082	0	15604	8560	0	7044	1693	1631	0	62	10.85	19.05	NaN	0.88	1509	437457	9874	2.26	405	4.1	57065	7718	7529	13.52	16.35	766	9.92	+	0.83142	1.1159	0.58068	0.81263	
20190902_JH_EV_Ubi_2	902_JH_EV_Ubi_2	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term);GlyGly (K);Deamidation (NQ)	Carbamidomethyl (C)			False	True	1	2		Standard		7099	8675	0	11130	6220	0	4910	1220	1170	0	50	10.96	18.81	NaN	1.02	1073	671763	7160	1.07	351	4.9	67411	5595	5441	8.3	11.65	563	10.06	+	0.83409	1.1139	0.57459	0.7806	
20190902_JH_EV_Ubi_3	902_JH_EV_Ubi_3	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term);GlyGly (K);Deamidation (NQ)	Carbamidomethyl (C)			False	True	1	2		Standard		7201	8980	0	11550	6410	0	5140	1225	1179	0	46	10.61	18.39	NaN	0.89	1089	706551	7442	1.05	340	4.57	72539	5789	5635	7.98	11.44	564	9.74	+	0.81338	1.0848	0.57188	0.77572	
20190821_JH_MUT_Ubi	821_JH_MUT_Ubi	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term);GlyGly (K);Deamidation (NQ)	Carbamidomethyl (C)			False	True	1	2		Standard		3723	12879	0	16509	9249	0	7260	2284	2212	0	72	13.83	23.92	NaN	0.99	1955	404637	10504	2.6	495	4.71	57588	8226	7982	14.28	16.31	909	11.05	+	0.75181	1.0078	0.55227	0.77705	
20190902_JH_MUT_Ubi_2	902_JH_MUT_Ubi_2	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term);GlyGly (K);Deamidation (NQ)	Carbamidomethyl (C)			False	True	1	2		Standard		5487	11813	0	15182	8444	0	6738	1922	1865	0	57	12.66	22.09	NaN	0.85	1628	565934	9698	1.71	457	4.71	67417	7594	7412	11.26	14.05	773	10.18	+	0.81809	1.074	0.58102	0.79415	
20190902_JH_MUT_Ubi_3	902_JH_MUT_Ubi_3	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term);GlyGly (K);Deamidation (NQ)	Carbamidomethyl (C)			False	True	1	2		Standard		4838	11106	0	14389	7823	0	6566	1717	1648	0	69	11.93	21.07	NaN	1.05	1440	501054	9024	1.8	467	5.18	59040	6896	6697	11.68	14.48	806	11.69	+	0.81489	1.0649	0.57471	0.78763	
20190821_JH_WT_Ubi	821_JH_WT_Ubi	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term);GlyGly (K);Deamidation (NQ)	Carbamidomethyl (C)			False	True	1	2		Standard		4424	13612	0	17310	9914	0	7396	2874	2769	0	105	16.6	27.93	NaN	1.42	2556	524244	11313	2.16	446	3.94	75542	9030	8784	11.95	14.07	811	8.98	+	0.74463	0.99363	0.54633	0.76418	
20190902_JH_WT_Ubi_2	902_JH_WT_Ubi_2	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term);GlyGly (K);Deamidation (NQ)	Carbamidomethyl (C)			False	True	1	2		Standard		7122	12027	0	15246	8808	0	6438	2345	2248	0	97	15.38	25.52	NaN	1.51	2073	724210	10128	1.4	389	3.84	84660	7998	7808	9.45	11.97	738	9.23	+	0.74887	1.0252	0.51992	0.74191	
20190902_JH_WT_Ubi_3	902_JH_WT_Ubi_3	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term);GlyGly (K);Deamidation (NQ)	Carbamidomethyl (C)			False	True	1	2		Standard		6800	11555	0	14686	8424	0	6262	2277	2187	0	90	15.5	25.96	NaN	1.44	1984	711143	9626	1.35	426	4.43	83876	7620	7414	9.08	11.45	730	9.58	+	0.75071	1.0115	0.53799	0.76709	
Total																		51342	102729	0	131606	73852	0	57754	17557	16909	0	648	13.34	22.9	NaN	1.12	5227	5246993					625138	66466	64702	10.63	13.41	6660	10.02		0.78124	1.0452	0.55616	0.77573