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
22-052-Murphy-control-1	Control 1	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		10700	28117	0	36417	19817	0	16600	112	112	0	0	0.31	0.57	0	0	92	1039183	22060	2.1	2305	10	70059	15091	11274	22	23	2318	15	+	0.70006	0.88529	0.39806	0.50369	
22-052-Murphy-control-2	Control 2	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		10422	30693	0	39423	21963	0	17460	137	135	0	2	0.35	0.61	0	0.011	113	1073051	24264	2.3	2566	11	73741	16796	12648	23	24	2669	16	+	0.64553	0.81587	0.37166	0.48215	
22-052-Murphy-control-3	Control 3	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		9699	36764	0	47464	26064	0	21400	164	160	0	4	0.35	0.61	0	0.019	144	1034999	30058	2.9	2906	9.7	74925	20216	15562	27	29	3359	17	+	0.59974	0.7439	0.34467	0.44534	
22-052-Murphy-SHP20infil-1	SHP20 Infil 1	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		7994	53989	0	75974	32004	0	43970	138	133	0	5	0.18	0.42	0	0.011	106	736125	41175	5.6	5223	13	56375	23270	16384	41	44	4823	21	+	0.51876	0.649	0.30743	0.38844	
22-052-Murphy-SHP20infil-2	SHP20 Infil 2	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		7534	58543	0	82010	35076	0	46934	189	184	0	5	0.23	0.52	0	0.011	125	791363	45526	5.8	5722	13	64024	25862	18192	40	42	5161	20	+	0.44526	0.62439	0.2723	0.39228	
22-052-Murphy-SHP20infil-3	SHP20 Infil 3	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		6626	67802	0	95204	40400	0	54804	292	273	0	19	0.31	0.68	0	0.035	181	928839	52156	5.6	7017	13	79259	29870	19109	38	38	5908	20	+	0.46885	0.61975	0.29051	0.39621	
22-052-Murphy-SHP20-LL-1	SHP20 LL 1	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		7783	56224	0	77430	35018	0	42412	163	157	0	6	0.21	0.45	0	0.014	105	942621	43193	4.6	5540	13	75482	25909	18476	34	36	5012	19	+	0.44709	0.58199	0.27167	0.3661	
22-052-Murphy-SHP20-LL-2	SHP20 LL 2	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		8905	44780	0	60073	29485	0	30588	94	87	0	7	0.16	0.3	0	0.023	71	887237	34609	3.9	4300	12	62043	21854	16627	35	40	4170	19	+	0.66346	0.94818	0.43033	0.61231	
22-052-Murphy-SHP20-LL-3	SHP20 LL 3	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		8358	50095	0	67549	32639	0	34910	193	184	0	9	0.29	0.56	0	0.026	133	988293	38640	3.9	4899	13	77018	24254	17743	31	33	4659	19	+	0.49387	0.69061	0.28348	0.38936	
22-052-Murphy-SHP20-PEI-infil-1	PEI Infil 1	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		9034	44627	0	61317	27937	0	33380	158	143	0	15	0.26	0.51	0	0.045	117	859198	33670	3.9	4404	13	62381	20473	14258	33	35	3966	19	+	0.51546	0.68201	0.32393	0.44482	
22-052-Murphy-SHP20-PEI-infil-2	PEI Infil 2	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		9266	42418	0	59270	25566	0	33704	151	144	0	7	0.25	0.56	0	0.021	105	704003	32450	4.6	4190	13	47513	18499	13049	39	43	3840	21	+	0.43589	0.59589	0.25054	0.34513	
22-052-Murphy-SHP20-PEI-infil-3	PEI Infil 3	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		10085	34499	0	46521	22475	0	24046	92	87	0	5	0.2	0.39	0	0.021	75	824596	25819	3.1	3624	14	53983	16650	11099	31	34	3237	19	+	0.50317	0.62365	0.29036	0.35354	
22-052-Murphy-SHP20-PEI-LL-1	PEI LL 1	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		7864	54660	0	71364	37954	0	33410	419	403	0	16	0.59	1.1	0	0.048	299	1058434	45021	4.3	4542	10	92621	29498	23688	32	33	5235	18	+	0.56742	0.74789	0.34451	0.47019	
22-052-Murphy-SHP20-PEI-LL-2	PEI LL 2	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		8201	51278	0	66693	35863	0	30830	364	353	0	11	0.55	0.98	0	0.036	239	1118620	42467	3.8	4057	9.6	99136	28012	22767	28	29	4847	17	+	0.52738	0.705	0.31372	0.42483	
22-052-Murphy-SHP20-PEI-LL-3	PEI LL 3	Trypsin/P	Specific			False	Oxidation (M);Acetyl (Protein N-term)				False	False	1	2		Standard		8381	49549	0	64641	34457	0	30184	346	329	0	17	0.54	0.95	0	0.056	249	1087731	40218	3.7	4199	10	94668	26483	21609	28	29	4842	18	+	0.6293	0.85158	0.38225	0.53205	
Total																		130852	704038	0	951350	456718	0	494632	3012	2884	0	128	0.32	0.63	0	0.026	488	14074293					1083228	342737	252485	32	33	64046	19		0.54283	0.7249	0.32519	0.44423