Advanced mass spectrometry  software development and consulting

 Support
Polymerix
Poly32

Sierra Analytics
Modesto, CA
(209) 545-8506

Sierra@MassSpec.com

APEX SOFTWARE

Advanced software for

small molecule confirmation

 using chemical structure

View Apex brochure (.pdf file 252 KB)

Publications regarding Apex

•      Do you have samples you suspect contain “interesting” molecules?

•      Do you have chemical structures for them?

•      Did you acquire MS and/or MS/MS data?

•      Do you want to know if your molecules are really there?

 Apex has the answer!

Sierra Analytics’ new Apex software takes a different approach to small molecule confirmation.

Using advanced scoring algorithms based on chemical structure, Apex locates and identifies target molecules in complex mixtures.

Apex is very general-purpose.   Any problem of correlation of chemical structure with MS data may be solved using Apex.

•  Metabolite Identification

•  Combinatorial Chemistry

•  Confirmation of synthesis

• High-throughput Screening

Mass Spectra:  Apex reads raw data from

•  Agilent ChemStation

•  Applied Biosystems / Agilent Analyst

•  Bruker XMASS

•  JEOL LC and GC AccuTOF

• SCIEX Analyst

•  Thermo Xcalibur

•  Waters MassLynx

with support for

•  MS, MS/MS, and “zoom” scan

•  Positive and negative ion mode (or both)

•  Single or multiple charge states

•  Multiple adducts

•  Optional chromatographic separation

•  External chromatographic traces

Chemical Structures:  Apex supports industry-standard formats

•  MDL MOLFile and SD-File

•  ASCII chemical formula

Unlike other software that requires the user to enter target ions or other information prior to data acquisition, Apex takes a different approach.

Apex predicts mass spectral features from chemical structure and compares them to experimental data at full mass accuracy.  No information other than structure, spectra, and analysis parameters are required.

Using a variety of flexible scoring and correlation metrics, Apex quickly ranks and filters the most consistent target molecules.

Apex is designed for high-throughput applications.  Using imported sample lists, Apex can quickly analyze an entire series of samples, providing color-coded displays according to user-specified criteria.

All user-supplied columns in the sample list are imported and carried through into the user interface and the results file.  Apex augments this information with its own results, giving a complete record of the acquisition and processing.

Tabular results are saved using industry-standard XML format files, for easy import into XML-aware corporate databases and other application software.

Reports are generated directly into editable Microsoft Word 2003 format files.  The content and layout of reports may be customized using style sheet templates.

Some publications that mention Apex (also as .pdf files)

Identification of In-Vitro Metabolites of Indinavir using Automated LC/MS/MS Acquisition, In-Silico Prediction, and Structure-Based Data Analysis

Searching for in-vitro drug metabolites in lcms chromatograms without the aid of radiolabels

The Use of Exact Mass Measurements at High Resolution to Probe Structural Diversity in Complex Natural Product Extracts

Structure-Based Confirmation of Small Molecules in LC/MS Datasets: Application to Metabolite Identification

Semi-Automated Metabolite Identification Using Information-Dependent LC/MS/MS Acquisition, In-Silico Metabolite Prediction, and Structure-Based Data Processing