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PXD022169

PXD022169 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleComparative Evaluation of MaxQuant and Proteome Discoverer MS1-based Protein Quantification Tools
DescriptionMS1-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.
HostingRepositoryPRIDE
AnnounceDate2021-05-31
AnnouncementXMLSubmission_2021-05-31_07:41:00.893.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAntonio Palomba
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListiodoacetamide derivatized residue
InstrumentLTQ Orbitrap Velos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-10-26 02:12:42ID requested
12021-05-31 07:41:01announced
Publication List
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]
Keyword List
submitter keyword: accuracy, differential analysis, dynamic range, label-free quantification, mass spectrometry, precision, proteomics, sensitivity, specificity
Contact List
Daniela Pagnozzi
contact affiliationPorto Conte Ricerche, Tramariglio, Alghero, Italy
contact emailpagnozzi@portocontericerche.it
lab head
Antonio Palomba
contact affiliationPorto Conte Ricerche
contact emailpalomba@portocontericerche.it
dataset submitter
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Dataset FTP location
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