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
R6-1_Naive_10	R6-1_Naive_10	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		21941	97125	0	163753	30471	0	133282	4893	4398	0	495	3	14	0	0.37	1822	892116	65729	7.4	8612	13	47705	16242	13575	34	40	6175	38	+	0.30224	0.52158	0.19631	0.36223	
R6-1_Naive_14	R6-1_Naive_14	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		21247	100690	0	165374	36000	0	129374	7363	6880	0	483	4.5	19	0	0.37	2411	852896	68168	8	10375	15	55655	17386	15022	31	47	7507	43	+	0.32578	0.57259	0.21905	0.40964	
R6-1_Naive_15	R6-1_Naive_15	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		27655	59997	0	105671	14313	0	91358	2571	1946	0	625	2.4	14	0	0.68	735	844120	40351	4.8	4219	10	36287	8416	6408	23	29	2408	29	+	0.30419	0.57065	0.20085	0.41707	
R6-1_Naive_20	R6-1_Naive_20	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		25991	70930	0	122179	19667	0	102512	3379	2724	0	655	2.8	14	0	0.64	881	887970	48391	5.4	5548	11	40101	10704	8483	27	32	3291	31	+	0.30705	0.51126	0.2013	0.34894	
R6-1_Trained_8	R6-1_Trained_8	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		17629	126022	0	202505	49533	0	152972	9944	9255	0	689	4.9	19	0	0.45	2539	841932	85598	10	14703	17	50213	21891	19582	44	51	10309	47	+	0.35974	0.60153	0.23344	0.40954	
R6-1_Trained_9	R6-1_Trained_9	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		17439	129290	0	203612	54968	0	148644	13778	12797	0	981	6.8	23	0	0.66	3012	746793	83250	11	17269	21	48628	20335	18421	42	56	10785	53	+	0.40166	0.66003	0.25983	0.44977	
R6-1_Trained_13	R6-1_Trained_13	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		25201	75721	0	129964	21464	0	108500	3788	3301	0	487	2.9	15	0	0.45	1078	891714	52011	5.8	6151	12	41188	11623	9396	28	35	3915	34	+	0.27957	0.54806	0.17962	0.37242	
R6-1_Trained_19	R6-1_Trained_19	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		24198	82134	0	136953	27309	0	109644	5138	4509	0	629	3.8	17	0	0.57	1414	837011	56036	6.7	7582	14	42502	13699	11184	32	39	5139	38	+	0.26868	0.50313	0.17626	0.34975	
WT_Naive_7	WT_Naive_7	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		13630	155615	0	231335	79893	0	151442	19422	18587	0	835	8.4	23	0	0.55	6495	804584	105060	13	22385	21	59516	33272	31100	56	69	18884	57	+	0.3705	0.62533	0.24254	0.42693	
WT_Naive_12	WT_Naive_12	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		15374	145438	0	217030	73842	0	143188	23395	21680	0	1715	11	29	0	1.2	6917	676117	95738	14	21823	23	47096	28859	27250	61	73	16866	58	+	0.41553	0.68585	0.28192	0.48347	
WT_Naive_17	WT_Naive_17	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		21623	98483	0	162714	34250	0	128464	6807	6254	0	553	4.2	18	0	0.43	1670	838995	67029	8	10390	16	45912	15748	13847	34	44	6491	41	+	0.34126	0.59163	0.2177	0.39706	
WT_Naive_18	WT_Naive_18	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		26312	68976	0	119662	18270	0	101392	2755	2156	0	599	2.3	12	0	0.59	708	883046	46721	5.3	5039	11	39609	10133	7971	26	31	3067	30	+	0.27422	0.49003	0.19008	0.39501	
WT_Trained_2	WT_Trained_2	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		24659	80060	0	138168	21926	0	116242	3348	2612	0	736	2.4	12	0	0.63	1205	906620	53958	6	6078	11	45291	12860	10346	28	34	4131	32	+	0.31741	0.59146	0.21009	0.41624	
WT_Trained_6	WT_Trained_6	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		19549	112464	0	183176	41744	0	141432	9295	8682	0	613	5.1	21	0	0.43	2632	799989	75806	9.5	12450	16	43555	18692	16698	43	52	8735	47	+	0.37985	0.64224	0.24981	0.43526	
WT_Trained_11	WT_Trained_11	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		23188	88397	0	148831	27947	0	120884	5082	4448	0	634	3.4	16	0	0.52	1351	866862	60152	6.9	8245	14	42133	13794	11677	33	40	5268	38	+	0.33177	0.58754	0.20999	0.40048	
WT_Trained_16	WT_Trained_16	Trypsin/P	Specific			False	Oxidation (M);Acetyl (N-term);Deamidation (NQ);Gln->pyro-Glu;Glu->pyro-Glu;Carbamyl (N-term)	Carbamidomethyl (C)		Oxidation (M)	True	False	1	1		Standard		22393	93321	0	153722	32908	0	120814	6487	6014	0	473	4.2	18	0	0.39	1615	888373	63867	7.2	9416	15	44127	15461	13445	35	43	6361	41	+	0.32174	0.5587	0.20889	0.38683	
Total																		348029	1584663	0	2584649	584505	0	2000144	127445	116243	0	11202	4.9	20	0	0.56	9822	13459138					729518	269115	234405	37	46	119332	44		0.35717	0.61274	0.23527	0.42459