Proteome Discoverer protocols

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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 in pipelines

PMCID: 5765118
PMID: 29323256
DOI: 10.1038/s41598-017-18985-5

[…] state or charge state 1 were excluded. an underfill ratio of 1% was used., the ms raw files were searched using sequest and the output was further refined by percolator on the software platform proteome discoverer 1.4 (thermo) against the human uniprot database (90440 entries, including 23204 isoforms) and filtered to a 1% fdr cut off. a precursor ion mass tolerance of 10 ppm, and product […]

PMCID: 5774092
PMID: 29347954
DOI: 10.1186/s13071-018-2618-x

[…] were split when the program detected stop codons (*), undefined amino acids (x) or gaps (-). the search of ms/ms raw files against these databases was conducted using the sequest algorithm (proteome discoverer 1.3; thermo scientific) with the constraints previously described []. for peptide validation, the proteome discoverer 1.3 software was used by filtering based on the q-value […]

PMCID: 5826277
PMID: 29515544
DOI: 10.3389/fmicb.2018.00262

[…] selection for ms/ms was enabled to allow for detection of as many precursors as possible., raw data from the ms analysis was searched against ncbi s. aureus mssa476 using the sequest algorithm in proteome discoverer version 2.1 (). data were filtered to a 1% peptide and protein level false positive rate using a reverse database approach (). the area under the curve (auc)-based label free […]

PMCID: 5826526
PMID: 29481576
DOI: 10.1371/journal.pone.0193104

[…] toggled automatically between ms and ms/ms acquisition. ms/ms data acquisition and processing were performed by xcalibur™ software (thermofisher scientific, ma)., proteins were identified through proteome discoverer software (ver. 2.1, thermo fisher scientific) and a mouse (mus musculus) uniprot protein sequence database (75568 sequences, and 32232886 residues). the reviewed protein sequences […]

PMCID: 5874768
PMID: 29415455
DOI: 10.3390/proteomes6010009

[…] 2.0 kv; capillary temperature, 250 °c and isolation windows 4 m/z. all ms files (.raw) are accessible from the jpost repository at url:, all ms and ms/ms data were analyzed by proteome discoverer tm (v2.1, thermo) for protein and peptide identification with sequest ht algorithms. the data were queried against a uniprot/swiss-prot database (v2015-08; homo sapiens 20,203 […]

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Proteome Discoverer in publications

PMCID: 5955991
PMID: 29769566
DOI: 10.1038/s41598-018-25943-2

[…] 0.1% tfa solution prior to loading into an orbitrap fusion mass spectrometer. bioinformatic searches from swiss-prot were used to identify peptides, and a label-free precursor ion detection method (proteome discoverer, version 1.3; thermo scientific) was used for accurate mass measurements on proteins/peptides with specific retention times on precursors/fragments., standard deviations (s.d.) […]

PMCID: 5937903
PMID: 29605494
DOI: 10.1016/

[…] (scx) chromatography and analyzed on a ltq orbitrap velos mass spectrometer (thermo scientific). ms/ms spectra were searched against the refseq 40 database using mascot (matrix science) through proteome discoverer software (version 1.3, thermo scientific) to quantify proteins with respect to the within-itraq medians of log2 transformed and normalized reporter ion intensities derived […]

PMCID: 5951806
PMID: 29760386
DOI: 10.1038/s41467-018-04343-0

[…] 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 […]

PMCID: 5945628
PMID: 29748585
DOI: 10.1038/s41598-018-25883-x

[…] rslc c18 column (2 μm particles, 100 å pore size; thermo scientific). the ms/ms spectra from each nano-lc-ms/ms fraction were searched against a selected rat tissue database (swissprot) using the proteome discoverer 2.1 software (thermo scientific). the search criteria were as follows: tryptic digestion, one missed cleavage, carbamidomethylation (c) and tmt plex (k and n-terminal) were fixed […]

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

[…] energy of 34 v. dynamic exclusion of precursor ions was set to 35 s and the fixed first mass was set to m/z 110 to match the itraq reporter ions (m/z 114–117)., 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 […]

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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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