Dataset Information

Comparative Evaluation of MaxQuant and Proteome Discoverer MS1-based Protein Quantification Tools

ABSTRACT: MS1-based label-free quantification can compare precursor ion peaks across runs, allowing reproducible protein measurements. Among bioinformatic platforms enabling MS1-based quantification, MaxQuant (MQ) is one of the most used, while Proteome Discoverer (PD) has recently introduced the Minora tool. Here, we present a comparative evaluation of six MS1-based quantification methods available in MQ and PD. Intensity (MQ and PD) and area (PD only) of the precursor ion peaks were measured and then subjected or not to normalization. The six methods were applied to datasets simulating various differential proteomics scenarios and covering a wide range of protein abundance ratios and concentrations. PD outperformed MQ in terms of quantification yield, dynamic range, and reproducibility, although neither platform reached a fully satisfactory quality of measurements at low-concentration ranges. PD methods including normalization were the most accurate in estimating the abundance ratio between groups and the most sensitive when comparing groups with a narrow abundance ratio; on the contrary, MQ methods generally reached slightly higher specificity, accuracy, and precision values. Moreover, we found that applying an optimized log ratio-based threshold can maximize specificity, accuracy, and precision. Taken together, these results can help researchers choose the most appropriate MS1-based protein quantification strategy for their studies.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human) Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Antonio Palomba

LAB HEAD: Daniela Pagnozzi

PROVIDER: PXD022169 | Pride | 2021-05-31

REPOSITORIES: Pride

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Comparative Evaluation of MaxQuant and Proteome Discoverer MS1-Based Protein Quantification Tools.

Palomba Antonio A Abbondio Marcello M Fiorito Giovanni G Uzzau Sergio S Pagnozzi Daniela D Tanca Alessandro A

Journal of proteome research 20210526 7

MS1-based label-free quantification can compare precursor ion peaks across runs, allowing reproducible protein measurements. Among bioinformatic platforms enabling MS1-based quantification, MaxQuant (MQ) is one of the most used, while Proteome Discoverer (PD) has recently introduced the Minora tool. Here, we present a comparative evaluation of six MS1-based quantification methods available in MQ and PD. Intensity (MQ and PD) and area (PD only) of the precursor ion peaks were measured and then su ...[more]

PMID: 34038140

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			Action	DRS
	Database_1.fasta	Fasta
	Database_2.fasta	Fasta
	PXD001819_File_Name_Conversion.txt	Txt
	PXD001819_MQ.zip	Other
	PXD001819_PD-A.pdResult	Other