Raw file	Experiment	Enzyme	Enzyme mode	Enzyme first search	Enzyme mode first search	Use enzyme first search	Variable modifications	Variable modifications first search	Use variable modifications first search	Multiplicity	Max. missed cleavages	Labels0	LC-MS run type	Time-dependent recalibration	MS	MS/MS	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
20140516_Q1_SA_PaJa_HNstudent_Helafrt_300mMsaltwash_WT1	HeLa(MBD3)_300_0.5_1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9726	28857	31934	25780	0	6154	2951	2876	0	75	9.24	11.16	NaN	1.22	2091	1248468	25163	2.02	1952	7.76	140660	22129	21354	15.73	24.63	2060	9.31	+	0.93202	1.1631	0.57641	0.73528	
20140516_Q1_SA_PaJa_HNstudent_Helafrt_300mMsaltwash_WT2	HeLa(MBD3)_300_0.5_2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9867	27804	30925	24683	0	6242	3124	3063	0	61	10.1	12.41	NaN	0.98	2338	1129672	24649	2.18	1674	6.79	121355	21629	20787	17.82	24.54	1762	8.15	+	0.89205	1.1017	0.55961	0.72888	
20140516_Q1_SA_PaJa_HNstudent_Helafrt_300mMsaltwash_WT3	HeLa(MBD3)_300_0.5_3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		10005	27608	30701	24515	0	6186	3007	2944	0	63	9.79	12.01	NaN	1.02	2242	1142093	24508	2.15	1665	6.79	121906	21492	20649	17.63	24.26	1737	8.08	+	0.87527	1.0972	0.55443	0.73835	
20140516_Q1_SA_PaJa_HNstudent_Helafrt_MBD3gfp_300mMsaltwash_GFP1	MBD3_300_0.5_1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8546	31730	34680	28780	0	5900	4354	4321	0	33	12.55	15.01	NaN	0.56	2925	1047859	28513	2.72	1920	6.73	126268	25451	24769	20.16	27.06	2202	8.65	+	0.77105	0.98385	0.49784	0.67199	
20140516_Q1_SA_PaJa_HNstudent_Helafrt_MBD3gfp_300mMsaltwash_GFP2	MBD3_300_0.5_2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8151	33862	36417	31307	0	5110	6169	6080	0	89	16.94	19.42	NaN	1.74	4094	965207	30068	3.12	2273	7.56	125293	27256	26780	21.75	26.93	2635	9.67	+	0.72865	0.94982	0.46998	0.64018	
20140516_Q1_SA_PaJa_HNstudent_Helafrt_MBD3gfp_300mMsaltwash_GFP3	MBD3_300_0.5_3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8175	34566	37179	31953	0	5226	7030	6966	0	64	18.91	21.8	NaN	1.22	4346	976904	30475	3.12	2517	8.26	126225	27548	27068	21.82	26.85	2896	10.51	+	0.70461	0.93579	0.45893	0.64286	
20140516_Q1_SA_PaJa_MBstudent_Helafrt_1Msaltwash_WT1	HeLa(MBD3)_1000_0.5_1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8093	33748	36851	30645	0	6206	6377	6306	0	71	17.3	20.58	NaN	1.14	4490	1058329	30018	2.84	2084	6.94	140981	27069	26433	19.2	24.41	2281	8.43	+	0.88173	1.1266	0.56444	0.75687	
20140516_Q1_SA_PaJa_MBstudent_Helafrt_1Msaltwash_WT2	HeLa(MBD3)_1000_0.5_2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8834	31043	33866	28220	0	5646	4034	3957	0	77	11.91	14.02	NaN	1.36	2694	1057650	27441	2.59	2043	7.45	130051	24672	24005	18.97	24.72	2179	8.83	+	0.94889	1.1879	0.61211	0.81332	
20140516_Q1_SA_PaJa_MBstudent_Helafrt_1Msaltwash_WT3	HeLa(MBD3)_1000_0.5_3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8374	32137	34819	29455	0	5364	4407	4300	0	107	12.66	14.6	NaN	1.99	3103	1025576	28457	2.77	2038	7.16	133578	25759	25134	19.28	24.46	2221	8.62	+	0.96775	1.2005	0.61629	0.80056	
20140516_Q1_SA_PaJa_MBstudent_Helafrt_MBD3gfp_1Msaltwash_GFP1	MBD3_1000_0.5_1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		7815	35318	37772	32864	0	4908	7185	7063	0	122	19.02	21.49	NaN	2.49	4516	1025358	31072	3.03	2507	8.07	136625	28315	27850	20.72	26.36	2867	10.13	+	0.75545	0.98239	0.4947	0.68152	
20140516_Q1_SA_PaJa_MBstudent_Helafrt_MBD3gfp_1Msaltwash_GFP2	MBD3_1000_0.5_2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		7888	34979	37381	32577	0	4804	6452	6375	0	77	17.26	19.57	NaN	1.6	4062	982537	31165	3.17	2355	7.56	132374	28441	27998	21.49	26.06	2716	9.55	+	0.76053	1.0054	0.50072	0.69718	
20140516_Q1_SA_PaJa_MBstudent_Helafrt_MBD3gfp_1Msaltwash_GFP3	MBD3_1000_0.5_3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		7982	34814	37297	32331	0	4966	6371	6261	0	110	17.08	19.37	NaN	2.22	3961	997728	30916	3.1	2372	7.67	132784	28141	27663	21.19	26.11	2766	9.83	+	0.7806	1.015	0.51304	0.70558	
20140528_Q1_SA_PaJa_students_Helafrt_MBD3gfp_normalconditions_GFP1	MBD3_300_0.15_1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8163	32460	34934	29986	0	4948	5497	5435	0	62	15.74	18.13	NaN	1.25	3674	896731	26721	2.98	3274	12.25	108588	23796	23431	21.91	27.57	3665	15.4	+	0.65553	0.8507	0.41704	0.5604	
20140528_Q1_SA_PaJa_students_Helafrt_MBD3gfp_normalconditions_GFP2	MBD3_300_0.15_2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8408	32742	35230	30254	0	4976	6927	6865	0	62	19.66	22.69	NaN	1.25	4427	902150	27620	3.06	3153	11.42	110203	24680	24251	22.4	27.22	3591	14.55	+	0.66666	0.87311	0.43044	0.58897	
20140528_Q1_SA_PaJa_students_Helafrt_MBD3gfp_normalconditions_GFP3lessextract	MBD3_300_0.15_3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8849	30598	33178	28018	0	5160	5096	5016	0	80	15.36	17.9	NaN	1.55	3241	886018	25845	2.92	2842	11	99776	22846	22464	22.9	28.17	3327	14.56	+	0.7138	0.92526	0.46207	0.63564	
20140528_Q1_SA_PaJa_students_Helafrt_normalconditions_WT1	HeLa(MBD3)_300_0.15_1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9213	29193	31864	26522	0	5342	4286	4196	0	90	13.45	15.82	NaN	1.68	3211	1029922	24901	2.42	2466	9.9	113043	22076	21569	19.53	25.9	2731	12.37	+	0.81211	1.0256	0.52021	0.69253	
20140528_Q1_SA_PaJa_students_Helafrt_normalconditions_WT2	HeLa(MBD3)_300_0.15_2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9523	28774	31353	26195	0	5158	3451	3418	0	33	11.01	13.05	NaN	0.64	2626	977930	23045	2.36	2908	12.62	101406	20392	19913	20.11	25.72	3101	15.21	+	0.80435	1.0109	0.50205	0.65451	
20140528_Q1_SA_PaJa_students_Helafrt_normalconditions_WT3	HeLa(MBD3)_300_0.15_3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9331	30041	32630	27452	0	5178	4780	4703	0	77	14.65	17.13	NaN	1.49	3494	857509	23944	2.79	3144	13.13	98969	21200	20737	21.42	26.29	3331	15.71	+	0.69962	0.90114	0.43689	0.5814	
20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_MTA2gfp_GFP1	MTA2_300_0.15_1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9955	28679	31134	26224	0	4910	3753	3707	0	46	12.05	14.14	NaN	0.94	3000	1115745	25758	2.31	1786	6.93	123406	23278	22807	18.86	25.79	2005	8.61	+	0.88573	1.1075	0.58034	0.75673	
20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_MTA2gfp_GFP2	MTA2_300_0.15_2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		10055	28299	30607	25991	0	4616	3816	3784	0	32	12.47	14.56	NaN	0.69	3041	1132457	25560	2.26	1658	6.49	120400	23204	22736	19.27	25.72	1898	8.18	+	0.80762	1.0125	0.52622	0.69061	
20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_MTA2gfp_GFP3	MTA2_300_0.15_3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9821	29181	31385	26977	0	4408	4609	4547	0	62	14.69	16.86	NaN	1.41	3554	1058131	26445	2.5	1690	6.39	120824	24194	23774	20.02	25.75	1973	8.15	+	0.80699	1.0176	0.52417	0.6913	
20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_WT_GFP1	HeLa(MTA2)_300_0.15_1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		10421	27397	29726	25068	0	4658	3857	3800	0	57	12.98	15.16	NaN	1.22	3050	1201825	24699	2.06	1584	6.41	124423	22439	22028	18.03	24.75	1800	8.02	+	0.80414	1.0083	0.52426	0.68583	
20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_WT_GFP2	HeLa(MTA2)_300_0.15_2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		10053	28341	30583	26099	0	4484	4090	4029	0	61	13.37	15.44	NaN	1.36	3197	1151062	25627	2.23	1580	6.17	124321	23344	22940	18.78	25.25	1852	7.93	+	0.81705	1.018	0.52142	0.67439	
20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_WT_GFP3	HeLa(MTA2)_300_0.15_3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		10784	26389	28679	24099	0	4580	2979	2938	0	41	10.39	12.19	NaN	0.9	2337	1098032	23833	2.17	1537	6.45	112732	21545	21100	19.11	25.91	1763	8.18	+	0.8719	1.077	0.56353	0.72686	
HeLa(MBD3)_1000_0.5_1																													4490																		
HeLa(MBD3)_1000_0.5_2																													2694																		
HeLa(MBD3)_1000_0.5_3																													3103																		
HeLa(MBD3)_300_0.15_1																													3211																		
HeLa(MBD3)_300_0.15_2																													2626																		
HeLa(MBD3)_300_0.15_3																													3494																		
HeLa(MBD3)_300_0.5_1																													2091																		
HeLa(MBD3)_300_0.5_2																													2338																		
HeLa(MBD3)_300_0.5_3																													2242																		
HeLa(MTA2)_300_0.15_1																													3050																		
HeLa(MTA2)_300_0.15_2																													3197																		
HeLa(MTA2)_300_0.15_3																													2337																		
MBD3_1000_0.5_1																													4516																		
MBD3_1000_0.5_2																													4062																		
MBD3_1000_0.5_3																													3961																		
MBD3_300_0.15_1																													3674																		
MBD3_300_0.15_2																													4427																		
MBD3_300_0.15_3																													3241																		
MBD3_300_0.5_1																													2925																		
MBD3_300_0.5_2																													4094																		
MBD3_300_0.5_3																													4346																		
MTA2_300_0.15_1																													3000																		
MTA2_300_0.15_2																													3041																		
MTA2_300_0.15_3																													3554																		
Total															218032	738560	801125	675995	0	125130	114602	112950	0	1652	14.31	16.71	NaN	1.32	12296	24964893					2926191	580896	568240	19.85	25.84	59359	10.22		0.79259	1.0161	0.51038	0.68645	
