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 data sets simulating various differential proteomics scenarios and covering a wide range of protein abundance ratios and amounts. PD outperformed MQ in terms of quantification yield, dynamic range, and reproducibility, although neither platform reached a fully satisfactory quality of measurements at low-abundance 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.

Comparative Evaluation of MaxQuant and Proteome Discoverer MS1-Based Protein Quantification Tools / Palomba, A.; Abbondio, M.; Fiorito, G.; Uzzau, S.; Pagnozzi, D.; Tanca, A.. - In: JOURNAL OF PROTEOME RESEARCH. - ISSN 1535-3893. - 20:7(2021), pp. 3497-3507. [10.1021/acs.jproteome.1c00143]

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

Abbondio M.;Fiorito G.;Uzzau S.;Tanca A.
2021-01-01

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 data sets simulating various differential proteomics scenarios and covering a wide range of protein abundance ratios and amounts. PD outperformed MQ in terms of quantification yield, dynamic range, and reproducibility, although neither platform reached a fully satisfactory quality of measurements at low-abundance 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.
2021
Comparative Evaluation of MaxQuant and Proteome Discoverer MS1-Based Protein Quantification Tools / Palomba, A.; Abbondio, M.; Fiorito, G.; Uzzau, S.; Pagnozzi, D.; Tanca, A.. - In: JOURNAL OF PROTEOME RESEARCH. - ISSN 1535-3893. - 20:7(2021), pp. 3497-3507. [10.1021/acs.jproteome.1c00143]
File in questo prodotto:
Non ci sono file associati a questo prodotto.

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11388/248654
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 24
  • ???jsp.display-item.citation.isi??? 23
social impact