PXD022169

PXD022169 is an original dataset announced via ProteomeXchange.

Title	Comparative Evaluation of MaxQuant and Proteome Discoverer MS1-based Protein Quantification Tools
Description	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.
HostingRepository	PRIDE
AnnounceDate	2021-05-31
AnnouncementXML	Submission_2021-05-31_07:41:00.893.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Antonio Palomba
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2020-10-26 02:12:42	ID requested
⏵ 1	2021-05-31 07:41:01	announced

Palomba A, Abbondio M, Fiorito G, Uzzau S, Pagnozzi D, Tanca A, Comparative Evaluation of MaxQuant and Proteome Discoverer MS1-Based Protein Quantification Tools. J Proteome Res, 20(7):3497-3507(2021) [pubmed]

submitter keyword: accuracy, differential analysis, dynamic range, label-free quantification, mass spectrometry, precision, proteomics, sensitivity, specificity

Daniela Pagnozzi
contact affiliation	Porto Conte Ricerche, Tramariglio, Alghero, Italy
contact email	pagnozzi@portocontericerche.it
lab head
Antonio Palomba
contact affiliation	Porto Conte Ricerche
contact email	palomba@portocontericerche.it
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD022169
     1. Label: PRIDE project
     2. Name: Comparative Evaluation of MaxQuant and Proteome Discoverer MS1-based Protein Quantification Tools