Table 1.

Performance comparison of different sample preparation and data analysis steps. In bold are the best methods according to assessed criteria: peptide/protein count, host/dietary contamination, Firmicutes or Bacteroidetes representation, time efficiency, FDR, identification rate, taxon-assigned peptides and number of taxonomic identification precision. The performance status is displayed using minus sign for poor, equal sign for similar/no difference or plus sign for good performance

		Peptide/protein count	Host/dietary contamination	Firmicutes	Bacteroidetes	Time efficiency	FDR	Identification rate	Taxon assigned peptides	Precision
Centrifugation	LSC	+	-	-	+	-
	nLSC	-	+	+	-	+
Digestion	In-solution	+				-
	FASP	-				+
Search strategy	Single-step	-				+	+	-
	Two-step protein	+				-	–	+
	Two-step sections	+				–	-	+
	Two-step taxa	-				-	+	-
Taxon quantification	Kraken2					+			+	–
	Diamond					–			-	-
	Unipept					+			+	+