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chevron_left Database search Label-free protein quantification Peptide assignment validation Peak detection Libraries/frameworks Protein inference Peptide selection chevron_right

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DIA-Umpire specifications


Unique identifier OMICS_09684
Name DIA-Umpire
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Maintained Yes


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Publication for DIA-Umpire

DIA-Umpire citations


Cost effective generation of precise label free quantitative proteomes in high throughput by microLC and data independent acquisition

PMCID: 5847575
PMID: 29531254
DOI: 10.1038/s41598-018-22610-4

[…] (following standard approaches,), repeated injection of a sample mixture matching the actual sample matrix (‘exhaustion’), or by pseudo-ms/ms correlative precursor-fragment feature extraction using dia-umpire. the spectral libraries were generated following a previously optimized procedure at <1% fdr using a combination of x! tandem and comet search engines. the libraries were used […]


Statistical control of peptide and protein error rates in large scale targeted DIA analyses

PMCID: 5581544
PMID: 28825704
DOI: 10.1038/nmeth.4398

[…] swath2stats. another option is the application of non-parametric modeling strategies for computing posterior probabilities at the peptide- and protein-level, as have been adapted for dia analyses in dia-umpire, and swathprophet., alternatively, the q-value has been proposed for error estimation at the psm-level as well as on the protein-level. the q-value is a significance measure for analyte […]


Inference and quantification of peptidoforms in large sample cohorts by SWATH MS

PMCID: 5593115
PMID: 28604659
DOI: 10.1038/nbt.3908

[…] indicating that the lowered sensitivity of ipf compared to openswath originates from ambiguous lower intensity signals (). depicts the equivalent results using a dia library generated by dia-umpire, where ipf achieved similar relative performance metrics compared to the dda library, but due to the lower size of the input library, the absolute number of detected peptidoforms […]


Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data Independent Acquisitions (SWATH)

PMCID: 5059418
PMID: 27590315
DOI: 10.1007/s13361-016-1476-z

[…] spectrometric wiff files were first converted to mzml using the sciex data converter version 1.3, and subsequently mzml files were converted to mzxml files using proteowizard version 3.0.8851. the dia-umpire [] signal extraction module was used to process swath acquisitions, which detects correlated precursor and fragment ion features and assembles them into pseudo-tandem ms/ms spectra stored […]


“Plug and play” investigation of the human phosphoproteome by targeted high resolution mass spectrometry

PMCID: 5915315
PMID: 27018578
DOI: 10.1038/nmeth.3811

[…] and assembled into a normalized retention time database (humanphosphoproteomert.irtdb) using skyline., dia and prm: for spectrum-centric analysis of dia and prm mass spectrometry results, we used dia-umpire version 1.4 with default parameters to assemble pseudo-ms/ms spectra for the database search pipeline described above. peptide-centric analysis was performed using skyline. signal […]


Large scale determination of absolute phosphorylation stoichiometries in human cells by motif targeting quantitative proteomics

PMCID: 4389224
PMID: 25814448
DOI: 10.1038/ncomms7622

[…] via the pride partner repository with the data set identifier pxd000728., the peptide ion quantitation was performed based on ms1 feature intensity using the dda quantitation module from dia-umpire. the dda quantitation module accepts the standard mzxml format and starts with background subtraction and centroiding for each ms1 spectrum. the untargeted feature detection algorithm uses […]

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DIA-Umpire institution(s)
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada; Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada

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