Obtain the sample files - Proteome Discoverer Software - Obtain the sample files - Proteome Discoverer Software - Proteome Discoverer Software

Proteome Discoverer 3.1 Familiarization Guide
Product Tree
Desktop Software > Proteome Discoverer Software
Ardia Platform > Software > Proteome Discoverer Software
Document Type
User Guide
Software version
3.1
  • Proteome Discoverer 3.1
  • Copyright
  • Preface
  • Familiarization guide overview
  • Access documentation
  • Analysis of yeast gene knockouts by multiplexed reporter ion quantification
  • The reporter ions quantification example
  • Configure Proteome Discoverer for the study
  • Add the FASTA file to Proteome Discoverer
  • Download the FASTA file using Proteome Discoverer
  • Download the FASTA file from the UniProt website
  • Locate the FASTA file on the application media
  • Configure the quantification method
  • Create the study
  • Create the analysis
  • Set up the processing workflow
  • Set up the consensus workflow
  • Work with the results
  • Enrichment analysis of the results
  • Reporter ion quantification with phosphorylation
  • The reporter ions quantification with phosphorylation example
  • Configure Proteome Discoverer for the study
  • Add the FASTA file to Proteome Discoverer
  • Download the FASTA file using Proteome Discoverer
  • Download the FASTA file from the UniProt website
  • Locate the FASTA file on the application media
  • Configure the quantification method
  • Create the study
  • Create the analysis
  • Set up the processing workflow
  • The IMP-ptmRS algorithm
  • Set up the consensus workflow
  • Set up ratios and complete the analysis
  • Work with the results
  • Label-free quantitation with spiked-in proteins
  • Label-free quantitation example
  • Obtain the sample files
  • Configure Proteome Discoverer for the study
  • Add the FASTA files to Proteome Discoverer
  • Download the FASTA file using Proteome Discoverer
  • Download the FASTA file from UniProt website
  • Locate the FASTA file on the application media
  • Create the study
  • Configure the LFQ example study file
  • Create a study
  • Configure the analysis
  • Set up the processing workflow
  • Set up the consensus workflow
  • Set up the ratios and complete the analysis
  • Work with the results
  • Use the display filter to view E. coli proteins
  • View the distribution of protein ratios using scatter plots
  • View the raw quantitative information for individual peptides
  • SILAC 3plex of E. coli proteins mixed with known ratios
  • The precursor ions quantification example
  • Configure Proteome Discoverer for the study
  • Add the FASTA file to Proteome Discoverer
  • Download the FASTA file using Proteome Discoverer
  • Download the FASTA file from UniProt
  • Locate the FASTA file on the application media
  • Create the study
  • Create the analysis
  • Set up the processing workflow
  • Set up the consensus workflow
  • Confirm the ratios and starting the analysis
  • Work with the results
  • Access the results
  • Filter the results
  • Use the heat map
  • View quan spectra for given peptides
  • Analysis of yeast gene knockouts by multiplexed reporter ion quantification with two replicates
  • The reporter ions quantification example with a common channel
  • Configure Proteome Discoverer for the study
  • Add the FASTA file to Proteome Discoverer
  • Download the FASTA file using Proteome Discoverer
  • Download the FASTA file from the UniProt website
  • Locate the FASTA file on the application media
  • Configure the quantification method
  • Create the study
  • Create the analysis
  • Set up the processing workflow
  • Set up the consensus workflow
  • Work with the results
  • Data independent analysis of proteome mixtures using CHIMERYS
  • Data independent analysis of proteome mixtures using CHIMERYS example
  • Configure Proteome Discoverer for the study
  • Add the FASTA file to Proteome Discoverer
  • Download the FASTA file using Proteome Discoverer
  • Download the FASTA file from the UniProt website
  • Locate the FASTA file on the application media
  • Create the study
  • Create the analysis
  • Set up the Processing workflow
  • Set up the Consensus worflow
  • Set up the ratio and complete the analysis
  • Work with the results
  • View Sample Abundances
  • Use the display filter to view protein quan occupancy
  • Use a PCA and Loading Plot to identify E.coli proteins
  • Use the display filter to view E.coli proteins
  • View the distribution of protein ratios using scatter plots
  • View the raw quantitative information for individual peptides

The sample files are listed in Label-free quantitation example. You can obtain the sample files from the PRIDE archive https://ftp.pride.ebi.ac.uk/pride/data/archive/2015/03/PXD001385/.

Back to home page