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Proteome Discoverer specifications


Unique identifier OMICS_04551
Name Proteome Discoverer
Alternative name PD
Software type Package/Module
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Windows
License Commercial
Computer skills Medium
Version 2.1
Stability Stable
Mascot, Proteome Discover
Maintained No


  • Feature Mapper
  • LFQProfiler
  • Minora Feature Detector
  • Precuror Ions Quantifier
  • Precursor Ions Area Detector
  • Reporter Ions Quantifier
  • RNP(xl)


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Publication for Proteome Discoverer

Proteome Discoverer citations


Rapid labelling and covalent inhibition of intracellular native proteins using ligand directed N acyl N alkyl sulfonamide

Nat Commun
PMCID: 5951806
PMID: 29760386
DOI: 10.1038/s41467-018-04343-0
call_split See protocol

[…] intensity precursor ions. Multiple charged peptides were chosen for MS/MS experiments due to their good fragmentation characteristics. MS/MS spectra were interpreted, and peak lists were generated by Proteome Discoverer (Thermo Fisher Scientific). Searches were performed using the SEQUEST HT (Thermo Fisher Scientific) against the latest uniprot database for whole Human proteome (Homo sapi […]


Additional oxidative stress reroutes the global response of Aspergillus fumigatus to iron depletion

BMC Genomics
PMCID: 5946477
PMID: 29747589
DOI: 10.1186/s12864-018-4730-x

[…] Thermo raw files were processed by Proteome Discoverer 1.4 (Thermo). MS/MS spectra were searched against the AspGD protein database of A. fumigatus Af293 ( […]


Identification of a unique Radical SAM methyltransferase required for the sp3 C methylation of an arginine residue of methyl coenzyme M reductase

Sci Rep
PMCID: 5943407
PMID: 29743535
DOI: 10.1038/s41598-018-25716-x

[…] in the MS1 scan were calculated using the Minora Feature Detector node. Further quantification was performed using the consensus workflow performing retention time alignment and feature mapping. The Feature Mapper node groups detected features from the processing workflow allowing quantification across all raw files thereby performing gap filling. In ‘Peptide and Protein Filter’ node the minimum […]


Mutational disruption of the ABCC2 gene in fall armyworm, Spodoptera frugiperda, confers resistance to the Cry1Fa and Cry1A.105 insecticidal proteins

Sci Rep
PMCID: 5940765
PMID: 29740041
DOI: 10.1038/s41598-018-25491-9

[…] t as 1 × 105. For each sample, the injection volume was adjusted per the protein assay to load 1 µg on column. Three technical replicates were applied with each sample.Proteins were identified by the Proteome Discoverer (version 1.4; Thermo Fisher Scientific, Waltham, MA, USA). The S. frugiperda protein database (1,786 sequences) from uniport was combined with a S. frugiperda ABCC2 (SfABCC2) prote […]


Proteome wide analysis of Anopheles culicifacies mosquito midgut: new insights into the mechanism of refractoriness

BMC Genomics
PMCID: 5941458
PMID: 29739330
DOI: 10.1186/s12864-018-4729-3

[…] LC/MS/MS derived data were searched and analyzed using Proteome Discoverer 1.4 (Thermo Scientific). The acquired MS/MS data were searched against UniProt mosquito database, a well curated database using SEQUEST algorithm. Search parameters used: trypsin e […]


Cigarette smoke and chewing tobacco alter expression of different sets of miRNAs in oral keratinocytes

Sci Rep
PMCID: 5935709
PMID: 29728663
DOI: 10.1038/s41598-018-25498-2
call_split See protocol

[…] Proteome Discoverer (version software suite (Thermo Fisher Scientific) was used for MS/MS searches using SEQUEST and Mascot (version 2.4.1; Matrix 617 Science) algorithms againt NCBI RefSeq […]


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Proteome Discoverer institution(s)
Center for Bioinformatics, University of Tübingen, Tübingen, Germany; Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Group, University Medical Center Göttingen, Göttingen, Germany; Quantitative Biology Center, University of Tübingen, Tübingen, Germany; Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
Proteome Discoverer funding source(s)
Supported by the BMBF (de.NBI, grant no. 031 A535A); and by the European Union (MARINA, grant no. 236215).

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