I have a proteomics data obtained by performing LC/MS of control normal mouse and anticancer drug treated mouse. I have got some uncharacterised seqeunces of proteomics and lots of upregulated and downregulated protein expression. Can any scholar suggest what i can do with all that information i have using bioinformatics tools for the paper publication.
Your help is much appreciated.
https://apps.cytoscape.org/apps/massspeccollection
Download Cytoscape and install
Mass Spec Collection plugin
please check this: (1)https://bioconductor.org/packages/release/data/experiment/html/RforProteomics.html (R based)
it can be used to access :
mass-spectrometry proteomics data, manipulate and visualise it
how to process label-free and labelled quantitative data
how to analyse the quantitation data.
(2) Genoppi v3.0 (R based)
Genoppi is an interactive web application for analyzing and visualizing integrated experimental human proteomics data with genetics.
https://github.com/lagelab/Genoppi
(3) Philosopher : A data processing toolkit for shotgun proteomics.
https://prvst.github.io/philosopher/
tutorial:https://prvst.github.io/philosopher/tutorial.html
From my experience the best way to identify the function of your obtained sequences is BLAST ing in NCBI. For that go through the link https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome ...
You can find it in ncbi.nlm.nih.gov portal and then button BLAST. You'll be able to comb sequences pertinent with yours and compare. Even you can find expressed protein isoforms the sequences of which are closer to yours.
Another option try to contact with MASCOT database by installing its software. For that you'll need to provide LC/MS characteristics.
Good luck.
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