. Author manuscript; available in PMC: 2021 Dec 5.

Published in final edited form as: Nat Protoc. 2021 Oct 29:10.1038/s41596-021-00616-z. doi: 10.1038/s41596-021-00616-z

Table 2 ∣.

Maxquant settings

Parameter name	Setting
Variable search parameters
Group-specific paramters
→ Type	Standard
→ Variable modifications (All)	Acetyl (K) Acetyl (N-term)
→ Variable modifications: 11plex ONLY	Variable TMT10plex N-term^a Variable TMT10plex Lys^a
→ Variable modifications: 16plex ONLY^b	Variable TMTpro16plex N-term^a,b Variable TMTpro16plex Lys^a,b
All other parameters default
SCoPE2 search parameters
Group-specific paramters
→ Type	Reporter ion MS2: 11plex TMT or 16plex TMTpro^b
→ Variable modifications	Oxidation (M) Acetyl (Protein N-term)
→ Fixed modifications	None
Global parameters
→ Identification	PSM FDR: 1.00 (if using DART-ID) Protein FDR: 1.00 (if using DART-ID)
→ Advanced identification	Uncheck Second peptides
→ Advanced	Check Calculate peak properties
All other parameters default

MaxQuant adjustment from default settings for using MaxQuant to assess TMT labeling efficiency (Variable search) or for using MaxQuant to analyze SCoPE2 or 100xMaster data.

Custom modifications named per the included modifications.xml file.

TMTpro modifications are not included in the 1.6.7 release of MaxQuant. If you wish to search TMTpro 16plex data, a modifications .xml file and mqpar file to load the TMTpro reagents into Maxquant 1.6.7 are included in Supplementary Data 1.