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 # Vavassori_LNP2022_Proteomics
 
+Vavassori V, Ferrari S, Beretta S, et al.
+**Lipid nanoparticles improve ex vivo gene editing of human hematopoietic cells.**
+2022.
+
+Mass-Spectrometry based proteomic analysis on T cells derived from 3 healthy donors, constituting 3 biological replicates for CD40LG editing treated with LNPs. As controls, cells untreated (UT), mock electroporated or treated with LNPs formulated without RNA (Empty LNPs) were employed.
+
+- PRIDE: PXD037529
+
+---
+
+### Analyses ###
+
+Acquired raw data were analysed using MaxQuant, using the Andromeda search engine and a Human Fasta Database downloaded from UniprotKB.
+For both group-specific and global parameters, all values were kept as default.
+The LFQ intensity calculation was enabled, as well as the match between runs (MBRs) feature61. All proteins and peptides matching the reversed database were filtered out.
+Resulting data were analyzed using the R/Bioconductor package DEP.
+In details, protein quantification matrix from MaxQuant was processed and filtered keeping only proteins present in all replicates of at least one condition.
+Then, after normalization using a variance stabilizing transformation (vsn), the imputation of missing values was done using random draws from a Gaussian distribution centered around a minimal value.
+Differential Expressed Proteins (DEPs) among different tested conditions.
+
+Differential Expressed Proteins (DEPs) among different tested conditions were finally identified and the R/Bioconductor package ClusterProfiler was employed to perform pre-ranked Gene Set Enrichment Analysis (GSEA) on the Hallmark categories from the MSigDB.
+
+---
+
+### Directories and Files ###
+
+- _paper_plots.R_: script used to produce the plots of the paper;
+- _paper_data_: folder with data used to produce the plots of the paper.
+