Instead of using LFQ intensity values, users can choose to extract other data types such as iBAQ from the proteinGroups.txt file.
Users can now use *standard protein data file or *proteinGroups.txt as a input file in PROMOR App version 0.2.0
Link of PROMOR App: https://sgrbnf.shinyapps.io/PROMOR_App/
PROMOR App is an interactive web application to analyze and visualize label-free quantification (LFQ) proteomics data preprocessed using MaxQuant software.
PROMOR App also provides an option to build predictive models based on machine learning-based modeling.
PROMOR (PROtein MOdeling using R programming language) App is based on promor R package (https://caranathunge.github.io/promor/).
Users can use all options and parameters described in promor R package and do analysis using PROMOR App.
PROMOR App is developed to perform differential expression analysis of label-free quantification (LFQ) proteomics data and build predictive models based on machine learning-based modeling with top protein candidates.
PROMOR App provides a range of quality control and visualization tools at the protein level to analyze label-free proteomics data.
PROMOR App requires two Input files: one is proteinGroups.txt file produced by MaxQuant and second is an expDesign.txt which contains the experimental design of your proteomics data.
- proteinGroups.txt: This is one of the output files generated by MaxQuant program. It is a tab-delimited file that contains information on identified proteins from your peptide data.
OR
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Standard input file: This file should be a tab-delimited text file. Proteins or protein groups should be indicated by rows and samples by columns. Protein names should be listed in the first column and you may use a column name of your choice for the first column. The remaining sample column names should match the sample names indicated by the mq_label column in the expDesign.txt file.
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expDesign.txt: This is a tab-delimited text file that contains the design of your experiment. Note that you will have to create and provide this file when you run PROMOR App with your own data.
YouTube tutorial of PROMOR App without technical replicates data: https://www.youtube.com/watch?v=DWQeW74Lluo
YouTube tutorial of PROMOR App with technical replicates data: https://www.youtube.com/watch?v=iMXZFCmadc8
YouTube tutorial of PROMOR App with Modeling data: https://www.youtube.com/watch?v=m15gL-0vwC4