PhosphoFind provides functions to identify phosphorylation positions (aminoacid number in proteins) in phosphoproteomics experiments.

It assigns the phosphorylation site in protein

Phosphorylation landscape on time-resolved SYR1-dependent systemin signaling pathway

Some phosphoproteomics useful notebooks and sources

R codes for processing MS data

DeepRescore2: deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification

PhosNetVis is a web-based platform for integrated kinase enrichment analyses and interactive 2D/3D network visualizations of phosphoproteomics datasets.

Python pipeline to build empirical kinase networks and identify kinase signalling communities from quantitative phosphoproteomics data.

Clusters phosphoproteomics data based on a combination of the sequence information and abundance changes over conditions.

Custom analysis of in vitro circadian proteomics and phosphoproteomics using multiple sets of 10plex TMT with two genotypes

Estimate PTM hotspots in protein sequence alignments

PHOsphoproteomic dissecTiOn using Networks

An Ensemble Bioinformatic Platform to Empower Interactive Analysis of Quantitative Phosphoproteomics.

Analytical R Tools for Mass Spectrometry

A project for exploring differentially active signaling paths related to proteomics datasets

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)