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Protocols

ProMEX specifications

Information


Unique identifier OMICS_05988
Name ProMEX
Restrictions to use None
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Glycine max
    • Medicago truncatula
    • Zea mays

Publication for ProMEX

ProMEX citations

 (7)
library_books

System Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism

2017
Front Plant Sci
PMCID: 5491621
PMID: 28713396
DOI: 10.3389/fpls.2017.01066

[…] mation of the identified proteins were submitted to the public repository ProteomeXchange (Vizcaino et al., ) with the dataset identifier PXD003769 (http://www.proteomexchange.org/) as well as to the PROMEX database (http://promex.pph.univie.ac.at/promex/). Normalized spectral abundance factors (NSAFs) were calculated (Zybailov et al., ) for relative quantification. The protein candidates that are […]

library_books

Automated Protein Turnover Calculations from 15N Partial Metabolic Labeling LC/MS Shotgun Proteomics Data

2014
PLoS One
PMCID: 3988089
PMID: 24736476
DOI: 10.1371/journal.pone.0094692

[…] on with a text file containing peptide identification information. This algorithm has been implemented in a program, written in Python, which is freely available to the scientific community at http://promex.pph.univie.ac.at/protover. […]

call_split

Local inhibition of nitrogen fixation and nodule metabolism in drought stressed soybean

2013
J Exp Bot
PMCID: 3654410
PMID: 23580751
DOI: 10.1093/jxb/ert074
call_split See protocol

[…] tabase, downloaded from the Plant Gene Index Project, was employed using the Proteome Discoverer 1.2 software (Thermo Electron, San Jose, CA, USA). Protein and peptide information can be found in the ProMEX DB under the experimental ID ‘Gly max 001’ ().A decoy database enabled false-positive rate analysis. Only high-confidence peptides (false-positive rate <0.1%) with better than 5 ppm precursor m […]

library_books

Possible Role of Nutritional Priming for Early Salt and Drought Stress Responses in Medicago truncatula

2012
Front Plant Sci
PMCID: 3527748
PMID: 23267362
DOI: 10.3389/fpls.2012.00285

[…] y rate (FDR) Only high confidence (FDR ≤ 0.01%) peptide identifications with a minimum XCorr of 2.2 and proteins with at least two distinct peptides were considered. Peptide spectra are stored in the ProMEX library (Wienkoop et al., ) and can be checked under its ID “Med trun001.” Protein relative quantification is based on database dependent spectral counting as described previously (Larrainzar e […]

library_books

Identification of Novel in vivo MAP Kinase Substrates in Arabidopsis thaliana Through Use of Tandem Metal Oxide Affinity Chromatography*

2012
PMCID: 3567860
PMID: 23172892
DOI: 10.1074/mcp.M112.020560

[…] ares, which yielded 1′012 nonredundant phosphopeptides. These were mapped to 382 phosphoproteins. All pPSMs and corresponding MS/MS spectra can be found in PRIDE (http://www.ebi.ac.uk/pride/) and the ProMEX database (http://promex.pph.univie.ac.at/promex/). Tandem MOAC achieved a phosphopeptide enrichment of 55% (∑pPSM/∑PSM) and a phosphoprotein enrichment of 38% (∑P-proteins/∑Proteins). PD and MQ […]

call_split

Integration of Metabolomic and Proteomic Phenotypes

2008
PMCID: 2556022
PMID: 18445580
DOI: 10.1074/mcp.M700273-MCP200
call_split See protocol

[…] al. (2004) () the cumulative sum of recorded peptides per protein called spectral count was applied as a quantitative measure (). All the identified peptide product ion spectra can be downloaded from ProMEX to reveal identification criteria and to judge the quality of the spectra. ProMEX is a mass spectral reference library for plant proteomics and can be searched also with unknown samples (). […]


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ProMEX institution(s)
Department of Molecular Systems Biology, University of Vienna, Vienna, Austria

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