Determines the monoisotopic mass and charge state of parent ions from high resolution tandem mass spectrometry data. DeconMSn offers significant improvement for LTQ_FT and LTQ_Orbitrap instruments over the commercially delivered Thermo Fisher Scientific’s extract_msn tool. The software calculates the monoisotopic mass of the parent ion for each MSn spectrum by applying a modified THRASH approach to the parent isotopic distribution. For datasets with low-resolution MS1 spectra, it uses a support-vector machine based charge-detection algorithm to determine parent mass.
Allows annotated spectra from database search results to be viewed interactively. MS-Viewer is a spectral viewer that can be used for observing different types of peptide identification results. It can read Bibliospec and NIST msp format files, and can support viewing of spectral libraries. Moreover, this tool permits users to display annotated spectra thanks to MS-Product.
An interactive resource to the scientific community by integrating the massive peptide sequencing result from the draft map of the human proteome project. The Human Proteome Map was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. This includes 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues. The HPM portal provides an interactive web resource by reorganizing the label-free quantitative proteomic data set in a simple graphical view. In addition, the portal provides selected reaction monitoring (SRM) information for all peptides identified.
Assists in the development of web-based tools and data visualizations. phpMs contains functionalities for mzIdentML processing and visualization, and mascot generic format (MGF) format for mass spectrometry (MS) peak lists. It supplies objects that allow for the storage and manipulation of data, such as identification based objects including peptides and proteins, or spectra based objects such as precursor and fragment ions.
Extracts relevant metadata from an MSnSet instance. PRolocdata collects published protein-complex dataset and mass spectrometry-based spatial/organelle. The data are used through the two software pRoloc and pRolocGUI, and these data are handle by MSnSet. The MSnSet instances contain quantitative data and annotations (about sample and features). Users can also find experimental data.
Allows management and edition of mass spectral libraries in the field of metabolomics. mSpecs Editor provides capabilities for the automatic management and calculation of libraries though its scripting functionality. The graphical user interface (GUI) of this tool permits user to employ common techniques such as copy/paste, undo/redo and drag and drop.