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Informed-Proteomics specifications


Unique identifier OMICS_20109
Name Informed-Proteomics
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Some proteins.
Operating system Unix/Linux
Programming languages C#
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


  • MSPathFinder
  • PbfGen
  • ProMex



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  • person_outline Sangtae Kim <>
  • person_outline Samuel Payne <>

Publication for Informed-Proteomics

Informed-Proteomics in publications

PMCID: 5750139
PMID: 29172454
DOI: 10.1021/acs.analchem.7b04810

[…] characterization, and provides relative quantitation of multiple proteoforms in different experimental conditions. several other recently developed top-down proteomics software platforms, including informed-proteomics and protein goggle, can process etd spectra as well.−, in addition to development of these data analysis pipelines, new strategies for spectral interpretation of ms/ms spectra […]

PMCID: 5513976
PMID: 28769967
DOI: 10.3389/fpls.2017.01267

[…] of fully sequenced genomes and their functional annotation such as the universal protein resource (uniprot, or even of mass spectrometry spectral identification like promex (hummel et al., ; wienkoop et al., ). nevertheless, to date genomic databases for most plant model species, including legumes, lack proteome subcellular localization annotation (hooper et al., […]

PMCID: 5491621
PMID: 28713396
DOI: 10.3389/fpls.2017.01066

[…] of the identified proteins were submitted to the public repository proteomexchange (vizcaino et al., ) with the dataset identifier pxd003769 ( as well as to the promex database ( normalized spectral abundance factors (nsafs) were calculated (zybailov et al., ) for relative quantification. the protein candidates […]

PMCID: 5328390
PMID: 28326154
DOI: 10.1080/20002297.2016.1274582

[…] the overnight-cultured candida strains were diluted in dsm broth to a final od of 0.2 at 500 nm. the candida suspensions were stamped on the plates with a steers steel-pin replicator (cmi-promex icn, pedricktown, nj) and left to dry for 1 h at room temperature. the plates were subsequently aerobically incubated overnight at 37°c. as controls, the candida strains were also stamped […]

PMCID: 4894879
PMID: 27375629
DOI: 10.3389/fpls.2016.00750

[…] (username: [email protected], password: lhimleh6). furthermore all lotus proteomic data, annotated peptide spectra and experimental meta information is stored at the proteomics database promex (; )., principal component analysis (pca) and hierarchical clustering analysis were performed with the statistical tool box covain (). analysis of variance (one-way anova) was performed […]

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Informed-Proteomics institution(s)
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
Informed-Proteomics funding source(s)
Supported by the NIH National Institute of General Medical Sciences grant GM103493, the National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC) grant U24CA160019, the National Institute of Allergy and Infectious Diseases NIH/DHHS through interagency agreement Y1-A1-8401-01 (J. Adkins, PNNL), and the U.S. Department of Energy (DOE) Office of Science and Office of Biological and Environmental Research, under the Pan-omics program; by the “High Resolution and Mass Accuracy Capability” development project at the Environmental Molecular Science Laboratory (EMSL), a U.S. DOE national scientific user facility at Pacific Northwest National Laboratory (PNNL) in Richland, Washington.

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