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Centre for Protein Research Software

Licensed Software

Mascot (v2.5.1)

Software package for the interpretation and evaluation of mass spectometry-based proteomics data. Mascot is platform-independent search engine for sequence database dependent protein identification from MS-data. Mascot uses various raw data formats of which mgf, mzML and mzData are the most common. A range of workflows for protein quantification such as emPAI, iTRAQ, TMT, or SILAC are supported by the Mascot software. Our in-house Mascot server can be interrogated directly through the Mascot web interface from any computer within the University of Otago network. The Mascot server can also be accessed through the Proteome Discoverer and Protein Pilot software suites from dedicated local computers within the CPR network or from any computer within the University of Otago network through the Mascot Deamon.

Upon request we will provide users of the Centre for Protein Research with account and log in details to access the Mascot server at http://biocmascot.otago.ac.nz/mascot

Proteome Discoverer (v2.0)

Software package for the interpretation and evaluation of mass spectometry-based proteomics data. Within the Proteome Discoverer suite different search engines can be used in combination for more comprehensive sequence database searches. We have integrated the Mascot, Sequest HT and MS Amanda search engines. Besides sequence database-dependent search engines Proteome Discoverer also provides spectral library search options using the MSPepSearch and SpectraST programs. Workflows for quantification by peptide/protein labelling such as iTRAQ, ICAT, TMT or SILAC are supported. Label-free semi-quantitative proteomics can be performed using the Top3 approach or spectrum counts. The Proteome Discoverer software reads RAW, mgf, mzML, mzXML and DTA formats and can convert raw data into different MS data formats.

Protein Pilot (v4.5)

Software package for the interpretation and evaluation of mass spectometry-based proteomics data. The Protein Pilot software performs sequence database searches of MS/MS and LC-MS/MS raw data from various MS-platforms. The supported raw data formats are wiff, mgf or MALDI TOF/TOF raw data. Various workflows for protein quantification are available. The Paragon Search Algorithm is of particular interest when searching a large number of protein modifications as the number of allowed modifications to be searched dynamically is unlimited.

PeakView (v2.1) & SWATH (v2.0)

The PeakView software is used for viewing and manual interpretation of LC-MS/MS data generated by the 5600+ TripleTOF mass spectrometer. The SWATH plugin within the PeakView software provides a workflow for the compilation and viewing of SWATH data sets as well as the generation of spectral libraries and the export of intensity measurements of transitions, peptides and proteins into MarkerView for further statistical analyses.

The SWATH plugin within the PeakView software provides a workflow for the compilation and viewing of SWATH data sets as well as the generation of spectral libraries and the export of intensity measurements of transitions, peptides and proteins into MarkerView for further statistical analyses.

MarkerView (v1.2.1)

Protein quantification from data sets produced by multiple-reaction monitoring, parallel-reaction monitoring or SWATH-MS. 

SIEVE (v2.2)

Lable-free quantification of proteins/peptides, metabolites and other small molecules from high resolution/accurate mass LC-MS/MS data sets. SIEVE aligns ion chromatograms of multiple samples to identify accurate mass/retention time pairs between samples. The area under the curve of the monoisotopic peak is used for relative quantification. High resolution/accurate mass data (< 10 ppm error) generated by the Orbitrap system is required.

Xcalibur Suite (v2.0 SP1)

Programs within the Xcalibur package are used for viewing and manual interpretation of LC-MS/MS data generated by the LTQ-Orbitrap mass spectrometer. 

MetabolitePilot (v1.5)

Software suite for the analysis of mass spectrometry-based metabolomics data acquired by the 5600+ TripleTOF system. 

LipidView (v1.2)

Characterisation and quantification of lipids from 5600+ TripleTOF data sets. 

MultiQuant (v2.1)

Quantification of small molecules and other analytes from MRM/PRM data sets. 

Free Software

Skyline

Protein quantification from data produced by multiple-reaction monitoring, parallel-reaction monitoring or DIA (data-independent acquisition) experiments such as SWATH-MS. Workflows for absolute quantification using SIS-peptides are integrated as well. https://skyline.gs.washington.edu/labkey/project/home/begin.view?

Spectronaut

Analysis of DIA (data-independent acquisition) data sets such as SWATH-MS data; protein quantification by hyper-reaction monitoring. https://shop.biognosys.ch/spectronaut

Trans Proteomic Pipeline (TPP)

Software suite for the interpretation and evaluation of shotgun proteomics data; contains various software tools for statistics on shotgun data, the generation of spectral libraries as part of the SWATH workflow and MS-data format conversion. http://www.proteomecenter.org/software.php