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
1219576_PPI_Struc_Macrophages_A_DD_DDA_4_19Jan24_Cicero_BEHCoA-24-01-13	Mock_DD_DDA	Trypsin/P	Semispecific			False	Oxidation (M);Acetyl (Protein N-term)	Carbamidomethyl (C)			False	True	1	0		Standard		6714	52401	0	56791	48011	0	8780	16899	16404	0	495	30	34	0	5.6	16674	1135272	51831	4.6	386	0.74	191839	46912	46399	24	27	990	2.1	+	0.65863	0.93033	0.41623	0.61396	
1219628_PPI_Struc_Macrophages_B_DD_DDA_5_19Jan24_Cicero_BEHCoA-24-01-13	Mock_Macro_DD_DDA	Trypsin/P	Semispecific			False	Oxidation (M);Acetyl (Protein N-term)	Carbamidomethyl (C)			False	True	1	0		Standard		6756	51961	0	56436	47486	0	8950	15889	15461	0	428	28	33	0	4.8	15842	1109544	51402	4.6	399	0.78	187239	46340	45843	25	27	1047	2.3	+	0.65702	0.93712	0.41667	0.62027	
1219681_PPI_Struc_Macrophages_C_DD_DDA_6_19Jan24_Cicero_BEHCoA-24-01-13	Macro_DD_DDA	Trypsin/P	Semispecific			False	Oxidation (M);Acetyl (Protein N-term)	Carbamidomethyl (C)			False	True	1	0		Standard		6768	52056	0	56540	47572	0	8968	15410	14975	0	435	27	31	0	4.9	15196	1056163	51413	4.9	494	0.96	176700	46351	45818	26	29	1107	2.4	+	0.62571	0.89517	0.39882	0.59457	
Total																		20238	156418	0	169767	143069	0	26698	48198	46840	0	1358	28	33	0	5.1	27850	3300979					555778	139603	138060	25	28	3144	2.3		0.64759	0.92153	0.41082	0.60995	
