One of the key outputs from the Clinical Proteomic Technologies for Cancer initiative was the development of a number of novel software solutions to address challenges in proteomic data analysis. Below highlights several of the software products/algorithms developed by the program (or using data outputs from CPTC) with links to the Investigators’ sites for downloads.
ScanSifter is a software tool that assesses the quality of each raw spectrum and discards poor quality spectra.
ProteoWizard is a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomic data analysis.
MassQC is a software package that serves to diagnose liquid chromatography-mass spectrometry instrument hardware to ensure the instrument is running in a reproducible manner. Using data from CPTAC inter-lab studies, the National Institute of Standards and Technology developed a number of metrics to assess instrument performance and ProteomeSoftware subsequently built a graphical user interface to commercialize this tool.
MAZIE (Mass and Charge (Z) Interface Engine) is software that improves the identification of peptide ion mass and charge, based on the isotopic distribution of peptide ion envelopes.
DirecTag is a tag-based identification program, which can be used to recover protein sequences from tandem mass spectra.
IDPicker tool enables users to organize experimental data into complex hierarchies, which can be used for identifying candidate biomarkers in large cancer data sets.
iProphet allows integration of information supporting the identification of each unique peptide sequence from multiple MS/MS spectra.
Myrimatch is a tool designed to take experimental data from shotgun proteomic experiments and compare those spectra against sequences in a known database of proteins.
PepArML Meta-Search engine provides access to large-scale MS/MS sequence database searching infrastructure to researchers and labs without the computational resources or personnel to implement a distributed computing strategy in-house.
TagRecon is designed to complement database search tools by providing partial explanations for experimental data to assist in protein sequence identification.
PepCyber database focuses primarily on the interactions between binding domains in phosphoprotein binding proteins and phosphopeptides and can be used to help identify what post translational modifications are present.
QSpec is software designed to analyze differential protein expression data using label-free spectral count data and label-free peak intensity data.
SASPECT provides a function for identifying differentially expressed proteins between two sample groups using spectral counts from LC-MS/MS Experiments.
PEPPeR: A Platform for Experimental Proteomic Pattern Recognition, “PEPPeR” uses LC-MS data from mass spectrometers and combines pattern-based (unidentified peptide peaks) and identity-based (peptides sequenced via MS/MS) information to generate peptide quantitation.
XAlign is a Windows-based software used for recognizing peaks that have been generated by the same peptide that can be detected in different samples in the course of LC-MS experiments.
Enhanced Signature Peptide Predictor (ESP) is a computational method that uses protein physicochemical properties to select high-responding peptides and demonstrate its utility in identifying signature peptides in plasma, a complex proteome with a wide-range of protein concentrations.
Skyline is an open-source Windows client application for building Selected Reaction Monitoring Mass Spectrometry (SRM-MS) methods and analyzing the resulting mass spectrometric data.
MaRiMba software tool automates the creation of explicitly defined MRM transition lists required to program triple quadrupole mass spectrometers.