Search Results for "lc ms"
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Showing 44 open source projects for "lc ms"
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FSGSproteomics
Protepmics of Kidney biopsy tissues
...Objective: To investigate factors associated with the pathogenesis of FSGS and explore potential therapeutic targets. Methods: A total of 73 kidney biopsy tissues were analyzed by LC-MS/MS: FSGS (n=23), renal donors (n=14) as a healthy control group, and minimal change disease (n=15) and IgA nephropathy (n=21) as disease control groups. We validated the proteome data with immunohistochemistry and the Nephroseq microarray data. Results: Our proteomics platform identified a total of 4,168 proteins. A comparison between the FSGS with renal donor groups revealed 175 proteins increased -
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SpectralWorks
View, manipulate, analyze (LS fit, SVD, FT), and make figs of, spectra
Program for viewing, editing, manipulating, and analyzing absorbance spectra. Simple arithnetic includes making linear combinatins of up to 10 spectra. Advanced functions include fitting spectra as LC of standard basis spectra, singular value decomposition, Fourier transform, differentiation, integration, global fitting of 3D titration and kinetic data. Graphics features allow composing Figures and export to postscript files which can be converted to pdf, imported into photoshop for... -
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MSGraph is a program designed for the interactive, fast, qualitative analysis of mass spectrometric (MS) data. It is a tool to provide fast and simple access to all the information contained in an LC/MS analysis run.
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The package generates a feature table from a batch of LC/MS spectra in .cdf format. Instructions: http://www.sph.emory.edu/apLCMS/ References Bioinformatics. 25(15):1930-36. BMC Bioinformatics. 11:559.
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MS2Compound
Identification of custom metabolites from metabolomics data
This is a user friendly Graphical User Interface (GUI) for the identification of the compounds from LC-MS and LC-MS/MS metabolomics data. The tool allows use of custom database for the identification of compounds. The tool has been developed and maintained by Center for Systems Biology and Molecular Medicine (http://csbmm.yenepoya.res.in/), Yenepoya Research Centre, Yenepoya (Deemed to be University). -
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FAAC is an Advanced Audio Coder (MPEG2-AAC, MPEG4-AAC). The goal of FAAC is to explore the possibilities of AAC and exceed the quality of the currently best MP3 encoders. You can submit pull requests via GitHub: https://github.com/knik0/faac https://github.com/knik0/faad2
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An open source framework for LC-MS based proteomics and metabolomics. OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++. Our source code and wiki lives on GitHub (https://github.com/OpenMS/OpenMS).
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LC's Finder
A lightweight, cross-platform image manager
LCFinder (LC's Finder) is an image resource management tool that you can use to browse images, easily manage images, or search for images you want. As with the author's other projects, the naming is simple, it begins with LC, and the following Finder is referenced from the Finder in Mac OS. -
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LCUI
A small C library for building user interfaces with C, XML and CSS.
LCUI is a freely available software library to create GUI application, it is written in C, support the use XML and CSS describe the graphical interface, you can use it to make some simple effects. The above description and screenshots is for the version 1.0.0 (+), and the 1.0.0 version is still in development, it is not officially released, please do not use old versions of "files "page to download as version 1.0.0. -
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CFM-ID
Competitive Fragmentation Modeling for Metabolite Identification
Windows binaries and cross-platform source code for processing of EI-MS (GC-MS) and ESI-MS/MS (LC-MS) data for identification of metabolites. Includes tools for applying Competitive Fragmentation Modeling (CFM) to spectrum prediction and metabolite identification tasks, as well as a tool for fragment generation, and another for peak annotation. For further documenation see https://sourceforge.net/p/cfm-id/wiki/Home/ For related publications, and their associated supplementary data, please see https://sourceforge.net/p/cfm-id/wiki/Home/#related-publications There is also a web server supporting much of this functionality at http://cfmid.wishartlab.com For CFM3.0, please see http://cfmid3.wishartlab.com/. ... -
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...EigenMS utilizes SVD to detect bias trends in the data and eliminates them. EigenMS eliminates effects from known and unknown factors and can be utilized for any -omic platform. We have shown its utility in LC-MS/MS and metabolomics in the following two papers: 1) PMID: 19602524. "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition". Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, Smith RD, Dabney AR. Bioinformatics 2009 2) "Metabolomics data normalization with EigenMS" Karpievitch YV, Nikolic SB, Wilson R, Sharman JE, Edwards LM. ...
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GlycoPAT
Comprehensive, open-source tool for glycoproteomics MS data analysis
GlycoPAT is a modular, open-source MATLAB based toolbox for shotgun mass spectrometry based glycoproteomics data analysis. This program provides a novel platform for the streamlined analysis of traditional LC-MSn based high-throughput experimental data for the identification of site-specific N- and O-linked glycosylation on various proteins. More details are available at https://www.VirtualGlycome.org/glycopat Source code also available at https://github.com/kaichengub/GlycoPAT If... -
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MSqBAT
Label-free protein quantification for LC-MS
MSqBAT is a freely-available all-platform software application for label-free quantification of proteins from LS-MS data. It was developed in the lab of Dr. Christoph Rösli at the Heidelberg Institude for Stem Cells and Experimental Medicine (HI-STEM) and the German Cancer Research Center (DKFZ). It’s main features are 1) Label-free, MS1-based quantification 2) Support both LC-MALDI-MS- as well as LC-ESI-MS data 3) Supports both GeLC-MALDI-MS- and GeLC-ESI-MS data 4) Convenient, graphical user interface Acknowledgements The development of MSqBAT is kindly supported by YourKit Java Profiler. -
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The early version of this freeware (utility) transliterates ALA-LC romanized text to Arabic characters text. The latest version can transliterate from German DMG(DIN31635) and ALA-LC Arabic romanization standards.
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The Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research.
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MS2Browser
LC-MS/MS data browser designed for siderophore analysis
...NOTE: The program is written for personal use to assist siderophore analysis using high-resolution LC-MS/MS data. Please contact me if you have any questions about its use, bugs, etc. -
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ChelomEx
Isotope assisted discovery of metal chelating agents from LC-MS data
ChelomEx identifies chromatographic features of metal complexes and associated free ligands or other related adducts in high-resolution LC-MS data. A built-in graphical user interface and compound library aid in the efficient evaluation of the results. If you use ChelomEx for your research, please cite our Analytical Chemistry paper that describes the software (http://dx.doi.org/10.1021/ac503000e). To comment, send bug reports or suggestions for additional features to be implemented in future versions please send me a message. ... -
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Ionwinze
Spot the differences between samples, groups and classes
To download please go to Browse All Files for the complete pack! In mass spectrometry the detector responses are not always directly proportional to the quantity of compounds. Large peaks in LCMS traces are not equal to major components but their ionizability. The effectiveness of a medicinal plant, poisons in a mushroom, resistance and susceptibility to pest and diseases are not necessarily because of the compounds that give large peaks. These traits are determined by the different... -
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MetaOpen
Metabolomics Bioinformatics Tools
...This will facilitate the development of preventive, predictive and personalized medicine for specific diseases and will promote health and wellness. We use a number of high-throughput analytical platforms including multidimensional liquid chromatography-mass spectrometry (MDLC-MS) for proteomics, and for metabolomics; liquid chromatography-mass spectrometry (LC-MS), and comprehensive two-dimensional gas chromatography-mass spectrometry (GCxGC/TOF-MS). Each type of analysis affords limited analyte coverage of molecules present in a patient sample and therefore provides only a partial molecular profile for an individual patient. ... -
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iMet-Q (intelligent Metabolomic Quantitation) is an automated tool with friendly user interfaces for quantifying metabolites in full-scan liquid chromatography-mass spectrometry (LC-MS) data. It has a complete quantitation procedure for noise removal, peak detection and peak alignment. In addition to accurate quantitation, iMet-Q provides the charge states and isotope ratios of detected compounds. It accepts input data in netCDF, mzXML, and mzML format and exports quantitation results in csv and txt format. The software source code is freely available under the license of GPL2.
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MetTailor
MetTailor: Dynamic Block Summary and Data Normalization for Robust Ana
Mass spectrometry-based quantitative metabolomics (LC-MS or GC-MS) requires accurate peak alignment and adaptive normalization, both of which have known limitations in the current data extraction software packages. MetTailor is a software package that performs post-extraction processing steps such as cross-sample realignment and data normalization that are specifically designed to account for the experimental factors from chromatographic separation and MS analysis. ... -
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RT-alignment
Graph-based time alignment algorithms for multiple LC-MS datasets
Liquid chromatography coupled to mass spectrometry (LC-MS) is the dominant technological platform for proteomics. An LC-MS analysis of a complex biological sample can be visualized as a “map” of which the positional coordinates are the mass-to-charge ratio (m/z) and chromatographic retention time (RT) of the chemical species profiled. Label-free quantitative-proteomics requires the alignment and comparison of multiple LC-MS maps to ascertain the reproducibility of experiments or reveal proteome changes under different conditions. ... -
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HDP-Align
HDP-Align and various other alignment methods for LC-MS data
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MBMSearcher
Marine bacteria metabolite database
...With the support from the China Mineral Resources Research and Development Association (COMRRDA12SC01 and COMRRDA12SC02), a chemical database based on secondary metabolite profiles of marine bacteria together with an LC-MS matching software have been developed by Coastal Marine Laboratory (CML) of HKUST. >1000 bacterial strains collected from different marine environment have been successfully cultured and their secondary metabolites were analyzed by LC-MS and imported to database. This database and related software provide a new strategy for natural product screening and a complementary approach to current methods for marine bacteria identification. -
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..."Automated Annotation and Quantification of Glycans Using Liquid Chromatography Mass Spectrometry (LC-MS)." Bioinformatics, C.Y. Yu, A. Mayampurath, Y. Hu, Y. Mechref and H. Tang, Apr 2013
