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. 2023 Mar 22;22(5):100534. doi: 10.1016/j.mcpro.2023.100534

Table 1.

Label-free quantification overview (DDA-LFQ and DIA)

LC-MS/MS system FAIMS-Orbitrap Fusion Lumos Tribrid TripleTOF 6600
Acquisition (Quantification) FAIMS-DDA MS for label-free quantification at the MS1 level DIA MS for label-free quantification at the MS2 level
Protein groups quantified (≥2 peptides, 1% FDR) 6294 3106
Upregulated protein groups HD-MSN versus C116-MSN 443 (1% FDR and logFC absolute value >0.58) 96 (q-value <0.05 and logFC absolute value >0.58)
Downregulated protein groups HD-MSN versus C116-MSN 458 (1% FDR and logFC absolute value >0.58) 66 (q-value <0.05 and logFC absolute value >0.58)

Abbreviations: DDA, data-dependent acquisition; DIA, data-independent acquisition; FDR, false discovery rate; LFQ, label-free quantification; logFC, log2 fold change.