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.
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.
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.
Simplifies the construction of high quality custom spectral libraries. Curatr is complementary to mass spectrometry visualization tools, spectral matching software, online data analysis and sharing platforms, and repositories. It has several features: (1) it collects information about standards analyzed, (2) it automatically selects candidate tandem mass spectrometry (MS/MS) spectra for standards, (3) it facilitates manual curation of MS/MS spectra through the web-browser, (4) it has a searchable catalogue of all spectra contained in the library, and (5) it provides export compatibility with major repositories and external software applications.
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.
A software tool that processes mass spectrometry tandem spectra (MS/MS) data for identification and classification of microorganisms. We have demonstrated, using MS/MS data of 81 samples, each composed of a single known microorganism, that the proposed pipeline can correctly identify microorganisms at least at the genus and species levels. We have also shown that the proposed pipeline computes accurate statistical significances, i.e., E-values for identified peptides and unified E-values for identified microorganisms.
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.
Generates spectral dictionaries by using the generating function of tandem mass spectra (MS/MS) borrowed from statistical mechanics. Spectral Dictionaries analyzes the peptide reconstructions and determines their statistical significance. Then, it generates a spectral dictionary for each spectrum and uses fast pattern matching to compare the spectral dictionary against the indexed database.
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.
Provides a range of tools which may be used on any spectrum page to manipulate or analyze user’s data. Spectral Workbench is a web-based software suite for collecting spectra, using Public Lab DIY spectrometer. It was developed by the Public Lab spectrometry project, an open source community that tries to develop low-cost spectrometers for a range of purposes.
Dr. Yashwanth Subbannayya obtained his M.Sc. degree in Medical Biochemistry from Manipal University. He qualified the competitive CSIR-UGC National Eligibility Test and joined the Institute of Bioinformatics, Bangalore as a UGC Junior Research Fellow. As part of his Ph.D. work, he studied the molecular mechanisms of gastric cancer in clinical specimens using quantitative proteomic technologies. This study, the results of which were published in Cancer Biology and Therapy, yielded a novel therapeutic target for gastric cancer- CAMKK2. Further, he also studied the serum proteome of gastric cancer patients and developed assays for potential markers using the revolutionary multiple reaction monitoring approach. The results of this study were published in Journal of Proteomics. In addition to his research work, he also trained extensively in sample preparation for mass spectrometry, fractionation techniques and gained expertise in quantitative proteomic techniques and data analysis. In addition, he also trained extensively in various validation platforms including immunohistochemsitry, multiple reaction monitoring and Western blot. He has also worked as a curator for several biological databases including NetPath, Human Protein Reference Database (HPRD) and Breast cancer database. His work in various research projects have yielded him 23 publications either as lead author or co-author in peer reviewed journals. He is a reviewer for the journal Proteomics.
Dr. Yashwanth Subbannayya joined the YU-IOB Center for Systems Biology and Molecular Medicine in June, 2015. During the initial period, his job consisted of assisting other personnel of the university in the establishment of YU-IOB Center for Systems Biology and Molecular Medicine. He was also involved in training of Ph.D. students in biological aspects. After the establishment of the center, he trained in cell culture techniques and metabolomics analysis. At YU-IOB CSBMM, he is studying the molecular mechanisms in various cancers including oral cancer. In addition, he is studying the molecular mechanisms as well as the metabolic constituents of traditional medicine formulations using mass spectrometry technologies. In June 2016, he convened the national symposium “Genomics in clinical practice: Future of precision medicine” held at Yenepoya University on June 1 and 2, 2016. The resource persons included 16 individuals from various academic organizations as well as industry. The symposium was attended by 218 participants from 24 institutions around India. He is a member of the Scientific Review Board of Yenepoya Research Centre where he facilitates timely scientific review of research projects.