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	300mMsaltwash_WT1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9726	28857	31934	25780	0	6154	3351	3272	0	79	10.49	12.69	NaN	1.28	2309	1248468	25163	2.02	1952	7.76	140660	22129	21354	15.73	24.63	2060	9.31	+	0.92831	1.1512	0.57239	0.73217	
20140516_Q1_SA_PaJa_HNstudent_Helafrt_300mMsaltwash_WT2	300mMsaltwash_WT2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9867	27804	30925	24683	0	6242	3563	3499	0	64	11.52	14.18	NaN	1.03	2606	1129672	24649	2.18	1674	6.79	121355	21629	20787	17.82	24.54	1762	8.15	+	0.90336	1.108	0.5592	0.72254	
20140516_Q1_SA_PaJa_HNstudent_Helafrt_300mMsaltwash_WT3	300mMsaltwash_WT3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		10005	27608	30701	24515	0	6186	3391	3324	0	67	11.05	13.56	NaN	1.08	2469	1142093	24508	2.15	1665	6.79	121906	21492	20649	17.63	24.26	1737	8.08	+	0.90191	1.1159	0.56338	0.73888	
20140516_Q1_SA_PaJa_HNstudent_Helafrt_MBD3gfp_300mMsaltwash_GFP1	300mMsaltwash_GFP1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8546	31730	34680	28780	0	5900	5040	4986	0	54	14.53	17.32	NaN	0.92	3266	1047859	28513	2.72	1920	6.73	126268	25451	24769	20.16	27.06	2202	8.65	+	0.74935	0.96769	0.47927	0.64815	
20140516_Q1_SA_PaJa_HNstudent_Helafrt_MBD3gfp_300mMsaltwash_GFP2	300mMsaltwash_GFP2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8151	33862	36417	31307	0	5110	6831	6739	0	92	18.76	21.53	NaN	1.8	4441	965207	30068	3.12	2273	7.56	125293	27256	26780	21.75	26.93	2635	9.67	+	0.72732	0.955	0.46772	0.64631	
20140516_Q1_SA_PaJa_HNstudent_Helafrt_MBD3gfp_300mMsaltwash_GFP3	300mMsaltwash_GFP3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8175	34566	37179	31953	0	5226	7695	7587	0	108	20.7	23.74	NaN	2.07	4635	976904	30475	3.12	2517	8.26	126225	27548	27068	21.82	26.85	2896	10.51	+	0.72764	0.95914	0.47558	0.66461	
20140516_Q1_SA_PaJa_MBstudent_Helafrt_1Msaltwash_WT1	1Msaltwash_WT1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8093	33748	36851	30645	0	6206	6739	6642	0	97	18.29	21.67	NaN	1.56	4698	1058329	30018	2.84	2084	6.94	140981	27069	26433	19.2	24.41	2281	8.43	+	0.91493	1.169	0.58693	0.79807	
20140516_Q1_SA_PaJa_MBstudent_Helafrt_1Msaltwash_WT2	1Msaltwash_WT2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8834	31043	33866	28220	0	5646	4385	4291	0	94	12.95	15.21	NaN	1.66	2877	1057650	27441	2.59	2043	7.45	130051	24672	24005	18.97	24.72	2179	8.83	+	0.93457	1.1685	0.59756	0.79475	
20140516_Q1_SA_PaJa_MBstudent_Helafrt_1Msaltwash_WT3	1Msaltwash_WT3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8374	32137	34819	29455	0	5364	4798	4692	0	106	13.78	15.93	NaN	1.98	3342	1025576	28457	2.77	2038	7.16	133578	25759	25134	19.28	24.46	2221	8.62	+	0.97455	1.219	0.61757	0.80923	
20140516_Q1_SA_PaJa_MBstudent_Helafrt_MBD3gfp_1Msaltwash_GFP1	1Msaltwash_GFP1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		7815	35318	37772	32864	0	4908	7785	7650	0	135	20.61	23.28	NaN	2.75	4793	1025358	31072	3.03	2507	8.07	136625	28315	27850	20.72	26.36	2867	10.13	+	0.7644	0.99487	0.50054	0.6879	
20140516_Q1_SA_PaJa_MBstudent_Helafrt_MBD3gfp_1Msaltwash_GFP2	1Msaltwash_GFP2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		7888	34979	37381	32577	0	4804	6864	6766	0	98	18.36	20.77	NaN	2.04	4252	982537	31165	3.17	2355	7.56	132374	28441	27998	21.49	26.06	2716	9.55	+	0.79511	1.0414	0.52736	0.73604	
20140516_Q1_SA_PaJa_MBstudent_Helafrt_MBD3gfp_1Msaltwash_GFP3	1Msaltwash_GFP3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		7982	34814	37297	32331	0	4966	6875	6734	0	141	18.43	20.83	NaN	2.84	4192	997728	30916	3.1	2372	7.67	132784	28141	27663	21.19	26.11	2766	9.83	+	0.80942	1.0505	0.53169	0.73217	
20140528_Q1_SA_PaJa_students_Helafrt_MBD3gfp_normalconditions_GFP1	normalcond_GFP1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8163	32460	34934	29986	0	4948	6321	6239	0	82	18.09	20.81	NaN	1.66	4155	896731	26721	2.98	3274	12.25	108588	23796	23431	21.91	27.57	3665	15.4	+	0.66009	0.86013	0.41696	0.56261	
20140528_Q1_SA_PaJa_students_Helafrt_MBD3gfp_normalconditions_GFP2	normalcond_GFP2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8408	32742	35230	30254	0	4976	7567	7490	0	77	21.48	24.76	NaN	1.55	4800	902150	27620	3.06	3153	11.42	110203	24680	24251	22.4	27.22	3591	14.55	+	0.68593	0.8921	0.442	0.60154	
20140528_Q1_SA_PaJa_students_Helafrt_MBD3gfp_normalconditions_GFP2tr	normalcond_GFP3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		8656	30624	32918	28330	0	4588	5486	5442	0	44	16.67	19.21	NaN	0.96	3472	855194	25895	3.03	2974	11.48	98041	23160	22789	23.62	28.14	3376	14.58	+	0.69687	0.8929	0.44523	0.59798	
20140528_Q1_SA_PaJa_students_Helafrt_normalconditions_WT1	normalcond_WT1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9213	29193	31864	26522	0	5342	4778	4682	0	96	14.99	17.65	NaN	1.8	3558	1029922	24901	2.42	2466	9.9	113043	22076	21569	19.53	25.9	2731	12.37	+	0.81887	1.0218	0.52153	0.69082	
20140528_Q1_SA_PaJa_students_Helafrt_normalconditions_WT2	normalcond_WT2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9523	28774	31353	26195	0	5158	3943	3898	0	45	12.58	14.88	NaN	0.87	2992	977930	23045	2.36	2908	12.62	101406	20392	19913	20.11	25.72	3101	15.21	+	0.81429	1.0161	0.50385	0.65184	
20140528_Q1_SA_PaJa_students_Helafrt_normalconditions_WT3	normalcond_WT3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9331	30041	32630	27452	0	5178	5421	5336	0	85	16.61	19.44	NaN	1.64	3913	857509	23944	2.79	3144	13.13	98969	21200	20737	21.42	26.29	3331	15.71	+	0.72005	0.92287	0.44504	0.58776	
20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_MTA2gfp_GFP1	MTA2gfp_GFP1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9955	28679	31134	26224	0	4910	4080	4023	0	57	13.1	15.34	NaN	1.16	3235	1115745	25758	2.31	1786	6.93	123406	23278	22807	18.86	25.79	2005	8.61	+	0.88383	1.1024	0.57268	0.74531	
20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_MTA2gfp_GFP2	MTA2gfp_GFP2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		10055	28299	30607	25991	0	4616	4302	4263	0	39	14.06	16.4	NaN	0.84	3383	1132457	25560	2.26	1658	6.49	120400	23204	22736	19.27	25.72	1898	8.18	+	0.81841	1.0256	0.5307	0.69602	
20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_MTA2gfp_GFP3	MTA2gfp_GFP3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		9821	29181	31385	26977	0	4408	5074	5006	0	68	16.17	18.56	NaN	1.54	3860	1058131	26445	2.5	1690	6.39	120824	24194	23774	20.02	25.75	1973	8.15	+	0.82041	1.0347	0.52812	0.69961	
20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_WT_GFP1	MTA2gfp_WT1	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		10421	27397	29726	25068	0	4658	4294	4230	0	64	14.45	16.87	NaN	1.37	3365	1201825	24699	2.06	1584	6.41	124423	22439	22028	18.03	24.75	1800	8.02	+	0.81848	1.0202	0.5279	0.68763	
20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_WT_GFP2	MTA2gfp_WT2	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		10053	28341	30583	26099	0	4484	4500	4438	0	62	14.71	17	NaN	1.38	3507	1151062	25627	2.23	1580	6.17	124321	23344	22940	18.78	25.25	1852	7.93	+	0.83247	1.0408	0.52969	0.69183	
20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_WT_GFP3	MTA2gfp_WT3	Trypsin/P	Specific			False	Acetyl (Protein N-term);Oxidation (M)		False	1	2		Standard		10784	26389	28679	24099	0	4580	3384	3334	0	50	11.8	13.83	NaN	1.09	2642	1098032	23833	2.17	1537	6.45	112732	21545	21100	19.11	25.91	1763	8.18	+	0.85463	1.0637	0.54698	0.71322	
1Msaltwash_GFP1																													4793																		
1Msaltwash_GFP2																													4252																		
1Msaltwash_GFP3																													4192																		
1Msaltwash_WT1																													4698																		
1Msaltwash_WT2																													2877																		
1Msaltwash_WT3																													3342																		
300mMsaltwash_GFP1																													3266																		
300mMsaltwash_GFP2																													4441																		
300mMsaltwash_GFP3																													4635																		
300mMsaltwash_WT1																													2309																		
300mMsaltwash_WT2																													2606																		
300mMsaltwash_WT3																													2469																		
MTA2gfp_GFP1																													3235																		
MTA2gfp_GFP2																													3383																		
MTA2gfp_GFP3																													3860																		
MTA2gfp_WT1																													3365																		
MTA2gfp_WT2																													3507																		
MTA2gfp_WT3																													2642																		
normalcond_GFP1																													4155																		
normalcond_GFP2																													4800																		
normalcond_GFP3																													3472																		
normalcond_WT1																													3558																		
normalcond_WT2																													2992																		
normalcond_WT3																													3913																		
Total															217839	738586	800865	676307	0	124558	126467	124563	0	1904	15.79	18.42	NaN	1.53	13326	24934069					2924456	581210	568565	19.87	25.84	59408	10.22		0.80279	1.027	0.51434	0.69219	
