Yates lab

ProteinClusterQuant

Protein Cluster Quant is a Java software for the analysis of complex proteomics samples (quantitative or not). It helps to reduce the redundancy of the peptide-to-protein relationship and to visualize the results in a bipartite network (Cytoscape).

PINT

PINT is a new comprehensive web-based system to store, visualize, and query experimental proteomics data obtained under different experimental conditions and projects. PINT provides a very powerful query system through the use of different proteomics-specific data query commands running over both the experimental features and external annotations of the detected protein lists (such as UniprotKB).

GlycoMSQuant

This is a Java stand-alone tool for the quantitation of glyco sites. It calculates the proportion of different glyco-PTMs in a protein of interest. It supports data from IP2 (quant compare output files) and MaxQuant.

CensusTMT2MSstatsTMT

Converter from Census TMT output file to the input of MSstatsTMT

DTASelect2PepXML

Converter from DTASelect to pepXML formats

IP2_File_Transfer

Giving some SSH credentials to a file server with the files of IP2, it will explore a given list of IP2 projects to get all RAW files and DTASelect files and transfer them to an external FTP site, such as MassIVE

luciphor_dtaselect_integrator

Program that integrates results from Luciphor (PTM localization scoring algorithm) into DTASelect output files.

pctsea-parent

PCTSEA (Proteomics Cell Type Enrichment Analysis) is a tool designed to statistically determine which cell types are significatively enriched in an input set of proteins with certain relative expression values. This process is done by using a database of datasets of RNASeq expression values from single cells from which the cell type is known (or predicted).

proteoform_dbIndex

extension of dbIndex module to index proteoforms

QuantParser

Parser for quantitative data from files created by Census software.

utilities

General Java util classes used across different projects

ViSEAGO_Shiny

CoPIT

Co-Purifying Protein Identification Technology (CoPIT) is a tool for the prediction of true interactors in single bait IP-MS

dbIndex

Indexing of FASTA files for searching peptide masses and sequences

Dilu

DTASelect2MzId

Data file format converter, from DTASelect-filter.txt files (output from DTASelect software) to mzIdentML version 1.1.0 and 1.2.0

DTASelectParser

Java parser for DTASelect output files

mokapot

Fast and flexible semi-supervised learning for peptide detection in Python

MzIdentMLParser

parser of mzIdentML files to read the data using the proteomics model from utilities artifact

P3

The Protein-Protein Predictor (P3) is a software for the prediction of real protein-protein interactions in multiple-bait IP-MS experiments

pcomplex

PCQ_GUI

ProteinAccessibilityCalculator

Based on Jmol, it calculates the surface accessibility of specific sites in a given protein. Optionally it measures the distances between specific atoms of specific sites in the structure of the protein

RadialTopologyViewer

RadialTopologyViewer performs a graphical visualization of a bait protein interactome derived from a co-immunoprecipitation experiment.

rt2dtaselect

Adds retention time to dtaselect output files, by reading it from ms2 (either in the local system or in a remote server)

TargetSeeker-MS

TargetSeeker-MS is a Bayesian Inference approach for drug target discovery, using protein fractionation coupled to mass spectrometry. It identifies proteins that are statistically significantly enriched via generating a noise-model using Bayesian Inference, which are measured with high reproducibility across a set of replicates.