Mass Spectrometer Software

Chromeleon™ 7.2 Chromatography Data System (CDS) Software

Streamline your laboratory workflow using Thermo Scientific™ Chromeleon™ 7.2 Chromatography Data System (CDS) software. This software delivers superior instrument control, automation, data processing, and more. The first CDS to unify the workflows for chromatography and routine quantitative mass spectrometry (MS) analysis, Chromeleon software provides full integration of Thermo Scientific gas chromatography (GC-MS/MS) and liquid chromatography (LC-MS/MS) instruments. Run your analyses in an enterprise environment—from method creation to final reporting

Enhance Your Workflow Using the Innovative Capabilities of Chromeleon 7 CDS software

  • Industry-leading multi-vendor control—supports over 400 different instrument modules from over 15 manufacturers
  • Full control for all Thermo Scientific chromatography and many Thermo Scientific MS instruments
  • Robust enterprise (client/server) environment with database file storage (SQL Server Express, SQL Server, or Oracle)
  • Secure, administrator-controlled user access and permissions to ensure data integrity and enable compliance with GxP and 21 CFR Part 11
  • Simplified run creation, including sequence, methods and reports, with one-click eWorkflows™
  • Automated pass/fail decisions during runs with Intelligent Run Control to get the analysis right the first time
  • Streamlined MS quantitation, data processing, and NIST spectral library screening
  • Integral Report Designer with customizable, spreadsheet-based report templates with advanced calculations and charting

    • TraceFinder™

    Offer increased flexibility and an array of capabilities in performing targeted screening and routine quantitation with either high resolution accurate mass (HRAM) and/or triple stage quadrupole (TSQ) mass spectrometers with Thermo Scientific™ TraceFinder™ Software. Not only does TraceFinder provide method development tools for all molecule types, it also generates new methods from existing data. From pharma/biopharma to food safety, from environmental safety to clinical research and forensic technology, TraceFinder ensures increased productivity for your analytical laboratory, enabling you to address analytical challenges today and tomorrow

    Discover the Unique Benefits of TraceFinder

  • Streamlined targeted screening and quantitation for all molecule types
  • Easy access to all necessary information for hundreds of molecules in seconds
  • Simplifies workflow-driven method setup with fully automated data acquisition, data processing, and reporting
  • High-resolution isolation (HRI) enables isolation of isobaric mass peaks for cleaner MSn spectra
  • Automates analyses with intelligent sequencing
  • Speeds data processing and reporting with compound database (CDB), smart calibration curves, library search capability, and custom reporting
  • Facilitates data review with multi-peak review capabilities, automatic retention time and ion ratio adjustment, and extensive flagging options
  • Provides quantitative, semi-quantitative, and screening workflows
  • Simplifies operation with system start-up and shut-down methods

    • Compound Discoverer™

    Streamline and customize data analysis with Thermo Scientific™ Compound Discoverer™ small molecule identification software. Compound Discoverer empowers researchers to strategically collect, organize, store and report data for both targeted and untargeted high resolution analyses. The software simplifies data processing with its ability to customize workflows, assemble data collected from multiple samples into one unified report, and integrate compound identification capabilities. Compound Discoverer also offers a suite of tools for metabolism, unknown metabolomics, impurities and degradants, extractables and leachables, environmental and food safety research, and forensic toxicology

    Extensive Toolset

  • Untargeted compound detection with isotope and adduct grouping
  • Unknown elemental composition based on high resolution information
  • Database searching using mzCloud™, Chemspider, KEGG or your own databases
  • Expected compound search, including dealkylation and dearylation predictions and transformation products
  • Structure elucidation using FISh (fragment ion search)
  • Compound scoring based on matching natural or artificial pattern(s)
  • Interactive PCA and differential analysis
  • Heat map-like tables for peak areas, ratios, log 2 fold change, CVs, p values and adjusted p-values
  • Visualization of spectral tree along with fragmentation annotations provides a pathway to structural elucidation
  • Interactive PCA, volcano plot, ANOVA, box-whisker and trend line plot

    • Mass Frontier™

    Transform mass spectral data into answers, quickly and easily using Thermo Scientific™ Mass Frontier™ spectral interpretation software. Mass Frontier software provides small-molecule structural elucidation for research into metabolism, metabolomics, forensics, natural products, impurities, and degradants. Innovative features simplify the management, evaluation, and interpretation of GC and LC mass spectral data. Mass Frontier software complements Thermo Scientific™ Compound Discoverer software for small molecule research applications

    Intelligent & Easy to Use

  • Predicts fragmentation and generates mechanistic pathways
  • Performs Fragment Ion search (FISh) and FISh Explanation for structurally related components
  • Annotates MSn spectral ion trees, automatically
  • Identifies small molecule structures quickly and confidently using MSn data combined with extensive literature coverage on fragmentation mechanisms
  • Assists de novo structural elucidation using spectra and spectral tree comparison tools
  • Provides customizable and fully searchable user libraries to store spectra, fragments, mechanisms, search results, and more
  • Sorts search results by spectral tree similarity, retention time, m/z value, and molecular formula using the Components Editor
  • Complements MetWorks automated metabolite identification software for the study of biotransformations
  • Complements MetQuest automated qual/quan metabolic screening software for simultaneous quan/qual drug metabolism and pharmacokinetic analysis

    • ToxFinder™

    Clinical researchers and forensic toxicologists no longer have to choose between optimum results and ease of use. Thermo Scientific™ ToxFinder™ software delivers highly accurate screening and semiquantitative analysis from either triple quadrupole or high-resolution, accurate-mass mass spectrometer data. Its experiment-specific workflows simplify operation by displaying only the features and parameters required for the experiment type selected. Data review is simple, yet powerful while the custom report designer provides WYSISYG customization

    Screening and quantitation in a single workflow

  • Triple quadrupole based selected-reaction monitoring (SRM) analyses
  • Orbitrap based – full-scan all-ions fragmentation (AIF) analyses
  • Hybrid quadrupole-Orbitrap based full-scan data dependent analyses
  • Confirmation with ion ratios
  • Confirmation with isotopes, fragments, library matching

    • Proteome Discoverer™

    Identify and quantify proteins in complex biological samples using Thermo Scientific™ Proteome Discoverer™ software. Proteome Discoverer software simplifies a wide range of proteomics workflows, from protein and peptide identification to PTM analysis to isobaric mass tagging and both SILAC and label-free quantitation. It supports multiple database search algorithms (SEQUEST, Z-Core, Mascot, and Byonic) and multiple dissociation techniques (CID, HCD, ETD, and EThcD) for more comprehensive analyses

    Productive and Expandable

  • Provides a choice of search algorithms (SEQUEST, Z-Core, Mascot Byonic, etc.) and can combine output from multiple algorithms to maximize and cross-validate results
  • Supports multiple dissociation techniques (CID, HCD, and ETD) for more complete coverage and confident identification of PTMs
  • Supports isobaric mass tagging (TMT, iTRAQ) and heavy-peptide techniques, enabling relative or absolute quantitation
  • Validates protein IDs with false discovery rate (FDR) determination
  • Automates data analysis, and simplifies MSn data analysis through wizards and customizable workflows
  • Facilitates data comparison, exchange, and verification with support for data standards developed by the HUPO Proteomics Standards Initiative (PSI)
  • Illustrates biological context by automatically annotating identified proteins with GO classifications, PTMs sites, and literature references from public databases
  • Fast, robust algorithms for peak selection and peptide quantification to extract the maximum possible information from quantitative proteomics studies
  • Obtain reliable statistics and validate quantification results visually

    • ProteinCenter™

    Quickly extract meaningful biological information from multiple, complex data sets within minutes using Thermo Scientific™ ProteinCenter software, a web-based data tool for interpreting proteomics data. ProteinCenter software will find salient trends in data to facilitate biological insights

    Accesss the Latest Data and >10 Million Non-redundant Proteins

  • Access a single database consolidated from >20 public databases including all historical data
  • Compare data sets with the latest, as well as outdated, protein sequences and annotations
  • Compare 20 or more samples simultaneously—independent of the searched database and its version
  • Compare protein lists from different databases against each other or international studies
  • Reduce complexity—group proteins based on peptides or sequence homology
  • Create exclusion lists and remove protein contamination

    • PepFinder™

    For biotherapeutic proteins to be effective, they must be produced in biologically active forms with proper folding and post-translation modifications (PTMs). Thermo Scientific™ PepFinder™ software provides accurate identification, in-depth characterization, and relative quantitation of biotherapeutic and other proteins from mass spectrometric data. It provides an automated workflows for glycopeptide identification, disulfide bond mapping, and quantification of PTMs. PepFinder software automates previously time-consuming manual processes, processing complex data and integrating the results into concise, informative reports

    Easier Experimental Setup

  • PepFinder software takes full advantage of mass spectrometer capabilities, supporting electron transfer dissociation (ETD) and higher-energy collisional dissociation (HCD) as well as collision-induced dissociation (CID)
  • PepFinder software provides fast, automated component detection - detection of peptide mass, retention time, and abundance. Multiple, unique component detection algorithms are tailored to different experiment and instrument types for faster, more accurate analyses
  • Error-tolerant search enables identification of unspecified modifications and amino acid substitutions. A fragmentation map can easily be generated for confirmation
  • PepFinder software automates the determination of disulfide bond linkages, a task extremely difficult to do manually. Mapping of disulfide bond linkages is achieved by processing non-reduced data files. No previous knowledge of the linkage sites is required, so novel linkages and potential disulfide bond scrambling can be identified and confirmed by MS/MS. Non-reduced and reduced data set can be compared for additional confidence
  • Comparison of multiple samples provides extra confidence in disulfide mapping experiments by facilitating comparison of non-reduced and reduced conditions
  • PepFinder software generates comprehensive, site-specific modification summaries and sequence coverage maps for targeted proteins, eliminating difficult, tedious manual summarization

    • Simglycan™

    Speed the characterization of complex glycans using SimGlycan™ software from PREMIER Biosoft. SimGlycan software processes and interprets the multi-stage/sequential (MSn) data produced by Thermo Scientific™ Mass Spectrometers, a capability essential to determining glycan heterogeneity and isomeric forms. The software automatically matches experimental mass spectra against a comprehensive database and generates a scored list of candidate structures. More relevant information about the proposed structure, including the glycan class, pathway and enzyme, is provided via interactive links

    Comprehensive Analyses

  • Supports all Thermo Scientific ion trap and Orbitrap™-based instruments performing glycan characterization
  • Processes MSn data to resolve glycan heterogeneity, branching patterns, and isobaric structures. Up to seven levels of MS fragmentation can be needed to differentiate between glycan structural isomers
  • Includes a database of over 22500 glycans to process and verify structures
  • Provides a wealth of relevant biological information for the probable glycan structure, including glycan class, reaction, pathway, and enzyme
  • Searches for glycans with various chemical derivatives used for reducing end modifications, even if the derivative is not available in the database
  • Identifies complex glycosaminoglycan structures, even when modified with substituents such as sulfate, phosphate, and ethanolamine
  • Determines cross-ring and double glycosidic cleavages, through a combination of permethyl derivatization and MSn data
  • Creates reports that include glycan characteristics such as ID, sequence, name, composition, mass, precursor ion m/z, class, reaction, pathway, glycan image and theoretical fragments with corresponding mass and m/z values
  • Exports images of glycan structures, fragments, and spectra as JPEG or PNG files

    • LipidSearch™

    Lipidomics is crucial to understanding cellular physiology and pathology, and lipid profiling for disease phenotype analysis is a rapidly growing area in translational medical research. LC/MS is a powerful technique for the identification and quantitation of cellular lipids. The Thermo Scientific™ LipidSearch™ Software processes LC-MS data, including the high-resolution accurate-mass data generated by Thermo Scientific™ Orbitrap™-based mass spectrometers, to make provide accurate lipid identification. It automatically integrates complex data into reports and dramatically reduces data analysis time

    Extensive Lipid Database for More Comprehensive Identification

  • Lipid database containing >1.5 million lipid ions and their predicted fragment ions
  • Identification algorithms for product ion, precursor ion, and neutral loss scans
  • The peak detection engine implemented in LipidSearch software can accommodate data from multiple types of mass spectrometers and multiple types of MS experiments. The combination of unique peak detection algorithms, tailored for each experiment and instrument type, and mass spectral processing functions ensures accurate peak detection for better identification and quantification
  • LipidSearch software includes a group-specific ID algorithm optimized for targeted identification and a comprehensive ID algorithm optimized for untargeted identification. The group-specific algorithm uses precursor ion scans and neutral loss scans to identify lipids based on the polar head groups or fatty acids. The comprehensive ID algorithm uses a combination of product ion scans and database matching to identify lipids. LipidSearch software also includes scoring algorithms to filter out lower probability results
  • Prior to quantitation, the extracted chromatographic peaks from each sample are aligned within a retention time window, ensuring more accurate quantitation