Search Results for "proteomics"

PANDA is a comprehensive and flexib tool for quantitative proteomics data analysis, which is developed based on our solid foundations in quantitative proteomics for years. Several novelties have been implemented in it. First, we implement the advantage algorithms of LFQuant (Proteomics 2012, 12, (23-24), 3475-84) and SILVER (Bioinformatics 2014, 30, (4), 586-7) into PANDA. Second, we consider the state-of-art concept of quantification reliability in this quantitative workflow. ...

ProteoWizard development moved to GitHub in 2018. The ProteoWizard Library is a set of software libraries and tools for rapid development of proteomics data analysis software. The libraries are cross-platform and built from the ground up using modern C++ techniques.

Morpheus is a mass spectrometry–based proteomics database search algorithm designed from the ground up for high-resolution tandem mass spectra. We have discovered that for high-resolution MS/MS, simple spectrum preprocessing and scoring performs superior to more complex algorithms originally developed for low-resolution MS/MS, such as Sequest, Mascot, and OMSSA. Morpheus is also very fast—up to nearly 5 times faster than OMSSA for large human datasets.

PeptideManager is aimed to help the pre-selection of unique peptide sequences for the design of targeted proteomics approaches. Its main advantage is to allow the presence of a host/background proteome (e.g., xenograft samples) during this peptide sequences selection. PeptideManager can build peptide sequences databases from various public repository (SwissProt/Trembl/UniProt, RefSeq, IPI) and various proteases. For any use, please refer to the publication: doi: 10.3389/fgene.2014.00305 http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00305/abstract

CPC Tools is a collection of open-source proteomics tools for use with mass spectrometry-based proteomics data sets. These tools were created by the Cardiovascular Proteomics Center of Boston University School of Medicine (Boston, MA). STRAP (Software Tool for Rapid Annotation of Proteins) automatically annotates a protein list with information that helps to interpret mass spectrometry data.

BigBang/Horizon is a proteomics data analysis pipeline with focus on the shotgun LC/MSMS workflow.

MSQuant is a tool for quantitative proteomics/mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.