List of software that may interest you if you are using Proline
ProteoRE (Proteomics Research Environment) is a Galaxy-based platform for the functional analysis and the exploration of proteomics and transcriptomics data in biomedical research; it allows researchers to apply a large range of dedicated bioinformatics tools and data analysis workflows on their data, share their analyses with others, and enable tiers to repeat the same analysis while keeping tracks of the overall process. Currently, ProteoRE comprises 18 tools organized into five subsections for: i) data manipulation; ii) human and iii ) mouse species database annotation; iv) functional analysis; and v) pathway analysis along with graphical representations. This version also includes Galaxy generic tools and some tools from the GalaxyP project that should be of great help for people who want to (re)process their MS-based proteomics data (e.g. peptide/protein identification).
Online software suite for mass spectrometry data analysis. It proposes a FASTA file generation toolbox, grid computing for OMSSA searches, grid computing for de novo + blastdb searches and extraction of Gene Ontology annotations. You will also find links for a dN-TOP Validation Tool and Recover, a MS/MS spectra viewer/extractor designed to extract “high quality” spectra from peaklist files.
Prostar is a software tool devoted to the processing of label-free relative quantitative proteomics data produced by bottom-up LC-MS/MS experiments. Built on R biostatistics routines and web-based graphical user interfaces (Shiny technology), it is free, open-source and distributed via the BioConductor initiative. It is suited to a large type of users, ranging from occasional (with the stand-alone versions) to systematic use on a large proteomics platform (thanks to its server deployment options). It was designed to fit to a large number of quantitative data formats (including MaxQuant and Proline). Prostar contains numerous procedures to preprocess quantitative data, i.e. filtering, normalization, missing value imputation, aggregation of peptide intensities into protein ones, and null hypothesis significance testing. Moreover, it proposes numerous data mining tools, ranging from exploratory statistics to GO analysis, as well as most importantly, tools to select the most likely differentially abundant proteins with a corresponding false discovery rate.
Shiny application for visualisation and analysis of intact protein MS 2D maps.
HDX-Viewer is an interactive 3D viewer of Hydrogen-Deuterium eXchange data.