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BenchTop/PBM Mass Spectrometry Library Search System

BenchTop/PBM Mass Spectrometry Library Search System
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LEGACT PRODUCT NOTICE: This is a legacy product, as it is no longer developed by Palisade and support is minimal. We instead recommend the NIST MS Search and NIST AMDIS programs included in the NIST MS Library for most library searching needs. The following page is provided for historical reasons or for anyone you may still need to acquire the BenchTop/PBM product for special circumstances. Contact us about your requirements. Note that NIST or commercial libraries require a special conversion to SPC format before use inside BenchTop/PBM.


BenchTop/PBM is a Windows-based library search system that performs computerized identification of mass spectral unknowns against reference libraries of mass spectra. It features a Probability Based Matching (PBM) algorithm that can perform sub-second searches of large databases (e.g. Wiley Registry), probability ranked match reliabilities, graphic display of chromatogram+MS data and search results, and graphic display of chemical structures. In addition, the BenchTop/PBM system contains a flexible parametric retrieval browser to query and view MS libraries.

Key Benefits
  • View and identify unknown spectra from virtually any mass spectrometer.
  • Probability Based Matching - Rapid and reliable search results with match probability and structure display.
  • Create and search against libraries of MS reference spectra (such as NIST, Wiley, and user-supplied libraries). Note: MS reference libraries are sold separately.
  • Includes a browser application to locate and display spectra/structures with a powerful parametric query capability.
  • Compatibility with a wide variety of data formats. Displays and identifies unknown data from virtually any mass spectrometer including Agilent, Thermo Finnigan, Micromass, Perkin-Elmer, Varian and others instruments (based in part on MassTransit technology).


The BenchTop/PBM Mass Spectrometry (MS) library search system is a reference library software that provides the powerful Probability Based Matching (PBM) search algorithm. Directly compatible with data from virtually any mass spectrometer (see Table 1), BenchTop/PBM search results are rapid, reliable and consistent, enabling BenchTop/PBM to perform an entire laboratory's unknown analyses regardless of the different mass spectrometer data sources.

In addition to proven PBM identification capabilities, BenchTop/PBM includes a host of options to provide user flexibility for data viewing and manipulating, PBM search refinement, custom library maintenance and Reference file browsing/querying.

GC/MS Display

  • Total Ion Chromatograms
  • Selected Ion Chromatograms
  • Chromatogram Zoom/Restore
  • Peak Averaging
  • Background Subtraction
  • Full Spectrum Display
  • Mass Scan w/ Instant Update
  • Mass Scan Zoom/Restore
  • Windows Copy/Paste
  • X, Y Scaling
  • Chemical Structure Display
  • Copy/Paste, Multiple Report Formats

PBM Search

  • Forward/Reverse Search Modes
  • Reliability Ranked Hit List
  • <1 Sec Search Time (Pentium)
  • Quadratic Scaling
  • Tabular/Graphic Search Results
  • Universal Data Compatibility
  • Adjustable Search Depth
  • Chemical Structure Display
  • Auto Peak Detection/Selection
  • Queued Searching
  • Copy/Paste Multiple Report Formats

Reference Browser

  • Name Prefix Query
  • Tabular/Graphic Spectrum Display
  • MW Query
  • CAS/Serial Query
  • Chemical Structure Display
  • Full/Partial Formula Query
  • Neutral Loss Query
  • User Library Create/Maintain
  • Name Fragment Query
  • Peak m/z and Abundance Query
  • Copy/Paste, Report Printing

BenchTop/PBM MS Library Search System includes

  • BenchTop/PBM v3.5 Windows Application
  • Mass Spectral Browser Windows Application
  • User's Guide

Note: Mass Spectral reference libraries for use with BenchTop/PBM must be obtained sparately. For example, the Wiley libraries and NIST may be used (but must be converted to PBM format first), as well as customer user-supplied libraries.

BenchTop/PBM Data File Read/Display/Search Capability

(Note: this list may not be up-to-date.)

Anelva AGS-7000 Finnigan SSX JEOL DA5000 Netzsch
Anelva DOS Fisons/VG 11-250 JEOL DA6000 Palisade
Balzers QuadStar 420 Fisons/VG JCAMP JEOL GCMate Perkin-Elmer Qmass 910
Balzers QuadStar 421 Fisons/VG LabBase/Trio JEOL JCAMP Perkin-Elmer TurboMass
EPA Fisons/VG MassLab JEOL MARIO Shimadzu PAC200
Extrel Merlin Fisons/VG Thermolab Kratos DS90 Shimadzu QP5000
Finnigan GCQ Hitachi NEC9810 Kratos/MSI MACH3 Shrader System
Finnigan Incos Hitachi 3DQ Mass Evolution Shrader for Windows
Finnigan ITS80 HP ChemStation MassLib JCAMP Teknivent Vector/1
Finnigan ITS40 HP RTE Nermag Automass Teknivent Vector/2
Finnigan Magnum JEOL Automass Nermag SIDAR Text
Finnigan MassLab JEOL Complement netCDF Varian Saturn


Figure 1. BenchTop/PBM displaying an unknown mixture (HP ChemStation data).

Figure 2. BenchTop/PBM identifies components of the complex mixture.

Figure 3. Browser Query

System Requirements

Microsoft Windows 9x/2000/NT or above.

Part No. Description Quantity
In Stock
US223204000EN BenchTop/PBM MS Search system (Palisade) INACTIVE------