Table 5 MaxQuant search library parameter settings.

From: Differential Proteome Analysis of Hybrid Bamboo (Bambusa pervariabilis × Dendrocalamopsis grandis) Under Fungal Stress (Arthrinium phaeospermum)

Item

Value

Type

Reporter ion MS2

Isobaric labels

TMT 6plex

Enzyme

Trypsin

Reporter mass tolerance

0.005 Da

Max Missed Cleavages

2

Main search Peptide Tolerance

4.5 ppm

First search Peptide Tolerance

20 ppm

MS/MS Tolerance

20 ppm

Fixed modifications

Carbamidomethyl (C)

Variable modifications

Oxidation (M), Acetyl (Protein N-term),

Database

Bamboo.fasta

Database pattern

Target-Reverse

PSM FDRa

≤0.01

Protein FDR

≤0.01

Protein quantification

Razor and unique peptides were used for protein quantification.

  1. aFDR = FP/ (FP + TP), FP (False Protein, from Decoy database) and TP (True Protein, from True database).
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