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About ProMass

Introduction:
Large biomolecules when ionized by electrospray (ESI) are predominantly multiply charged. When analyzed in the positive ion mode, peptides or proteins will be protonated at multiple sites as a result of the basic amino acids and amino terminus. On the other hand, oligonucleotides analyzed in the negative ion mode are de-protonated at multiple sites as a result of the acidic phosphate backbone. This multiple charging usually results in ESI mass spectra that contain a range of charge states. These complex spectra must be “deconvoluted” or “transformed” in order to order to determine the uncharged mass of the biomolecule. ProMass provides an automated platform for performing deconvolution of entire LC/MS data sets.

Overview:
ProMass is an automated biomolecule deconvolution and reporting software package that is used to process ESI/LC/MS data or single ESI mass spectra acquired on Thermo Scientific’s Xcalibur or Waters MassLynx data systems. ProMass was designed from the start for high-throughput applications. In fact, the normal way to run ProMass is through the Xcalibur or MassLynx sample list. Therefore, you can run a list of samples and have ProMass process them at the end or batch reprocess the list at your convenience.

ProMass uses a novel deconvolution algorithm known as ZNova that produces artifact-free deconvoluted mass spectra. ZNova can be used to process data from a wide variety of biomolecules including proteins, oligonucleotides, peptides, etc. Unlike many other deconvolution algorithms, ZNova can accommodate low charge state spectra and data of low signal-to-noise ratio. ProMass reports the results automatically in an easy-to-use and interactive format viewable from any web browser. A top-level summary page summarizes the results from multiple runs and displays them on a single hyperlinked page allowing you to navigate your results quickly. Target mass features allow you to search for multiple target masses from LC/MS data automatically. The target mass features include results color coding, allowing you to quickly hone in on the samples that may require further attention.

ProMass HR includes additional features for high-resolution data processing by incorporating the full suite of algorithms from Positive Probability Ltd (PPL).  ProMass HR methods can utilize the PPL algorithms that allow for monoisotopic mass determination of isotopically resolved mass spectra or enhanced resolution of isotopically unresolved mass spectra.  The PPL methods may be automated thru the same powerful mechanism as the standard version of ProMass.  Results are displayed through the same easy-to-use and intuitive web-based output as well.

Key Features of ProMass:
ProMass is more than just deconvolution software. ProMass is a tool that allows you to process and communicate your results in a highly collaborative web-based format.

  • Automated deconvolution of biomolecule mass spectra to determine molecular mass: applicable to proteins, peptides, oligonucleotides, etc.
  • Artifact-free deconvolution using proprietary ZNova algorithm, no manual intervention required to remove artifact peaks
  • Flexible processing of LC/MS peaks directed by Xcalibur processing method
  • Process data from a spectrum on the Windows clipboard
  • Automated web-based reporting, including summary report, chromatograms (UV and MS), raw, and deconvoluted mass spectra
  • Automatically calculate expected masses of target oligonucleotides and polypeptides
  • Color-coded results display, top-level summary report, and sample plate viewer allow for rapid visualization of your results
  • Automatically search for multiple target masses and report results in color-coded web-based summary
  • Excel-based summary report option
  • Automatic identification of terminal or internal fragments from oligonucleotide or protein sequences
  • Support for identifying fragments from multiple oligo or protein sequences (e.g., duplexes)
  • Support for specifying modified oligonucleotides
  • Support for “fuzzy” target masses such as PTM’s or protein drug conjugates
  • Dynamic sorting of columns in web-based reports
  • Target mass purity estimation computed from deconvolution peak intensities and chromatogram area percents
  • XML output
  • ProMass is currently available for Thermo Xcalibur , Waters MassLynx, and SCIEX data systems. Other data systems are in progress now.
  • A new web-based version is now available for you to try.

Additional Features of ProMass HR:
ProMass HR includes all of the features of the standard version of ProMass, plus the following:

  • Includes the full ReView PPL data processing package with ReSpect™ algorithms
  • Deisotoping for monoisotopic mass determination of isotopically resolved mass spectra for superior mass accuracy on HRAM data (e.g., <3 ppm on Orbitrap data).
  • Mass spectral peak shape modeling for enhanced resolution of isotopically unresolved mass spectra
  • PPL charge deconvolution algorithm for isotopically unresolved mass spectra
  • For more information, access our ProMass HR applications guide.

ProMass for Xcalibur System Requirements

You should follow the general system requirements for installing ProMass on the version of Xcalibur that you plan to use. The system requirements for running ProMass for Xcalibur are listed below:

  • Thermo Xcalibur v. 2.0.7 or later must be installed
  • The Thermo XDK (included on the Xcalibur CD) should be installed to enable the automation features
  • The required PC has the same requirements of the installed version of Thermo Xcalibur
  • Microsoft Windows XP through Windows 10 (limited by Xcalibur-Windows compatibility)
  • At least 110 MB of free disk space is required to install the program and help files

ProMass for SCIEX System Requirements

You should follow the general system requirements for the SCIEX OS for Windows compatibility.  The system requirements for running ProMass for SCIEX are listed below: