Proteome Discoverer protocols

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
Requirements Mascot, Proteome Discover
Maintained Yes


  • Feature Mapper
  • Minora Feature Detector
  • Precuror Ions Quantifier
  • Precursor Ions Area Detector
  • Reporter Ions Quantifier


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Proteome Discoverer IN pipelines

PMCID: 5885379
PMID: 29618380
DOI: 10.1186/s40425-018-0331-0

[…] multipole (normalized collision energy = 65)., mass spectrometry data was processed against the uniprot swiss-prot canonical mouse protein database (v. 2014_05, 16,669 sequences) with sequest ht in proteome discoverer v1.4 (thermo scientific). search settings were: monoisotopic parent ion mass tolerance of 1.25 da, monoisotopic fragment ion tolerance of 1.0 da, tryptic cleavage with up to 2 […]

PMCID: 5481877
PMID: 28649280
DOI: 10.1186/s13068-017-0844-7

[…] energy of 35%., mass spectra *.raw files were searched against an in—house specific database of the t. amestolkiae genome (10408 sequences, 5662098 residues) using the sequest search engine through proteome discoverer (version, thermo). precursor and fragments mass tolerance were set to 10 ppm and 0.5 da, respectively. search parameters included a maximum of two missed cleavages […]

PMCID: 5507865
PMID: 28701697
DOI: 10.1038/s41598-017-05355-4

[…] esi positive mode cal mix (mscal5 supelco, sigma-aldrich) as described previously19. the experiments were performed in duplicate., peptide identification was based on ms/ms data analysis in proteome discoverer 1.3.0339 (thermo fisher scientific inc., bremen, germany). search was performed against btg fasta database, with sequest algorithm. two missed trypsin cleavages were allowed per […]

PMCID: 5579227
PMID: 28860535
DOI: 10.1038/s41598-017-09973-w

[…] spectrometry was performed on a q exactive hf mass spectrometer (thermo fisher scientific, waltham, ma, usa) with a triversa nanomate (advion, ltd., harlow, uk) source in lc-chip coupling mode., proteome discoverer (v1.4, thermo scientific) was used for protein identification and the ms/ms spectra acquired were searched with sequest ht against the specific metagenome obtained for semiarid […]

PMCID: 5582647
PMID: 29246290
DOI: 10.1016/j.omtn.2017.08.007

[…] liquid chromatography (easy-nlc 1000, thermo scientific) and tandem mass spectrometry with an orbitrap velos pro mass spectrometer (thermo scientific). mathematical analyses were done with the proteome discoverer 1.3 software, sequest search engine and swissprot database, and maxquant 1.4 proteomic software. experiments were performed in triplicates., t.n.z. and a.s.k. conceived […]

Proteome Discoverer institution(s)
Thermo Fisher Scientific, San Jose, CA, USA

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