Cerno Home 2023

Accurate Mass Spectrometry Software Solutions

Cerno develops and publishes award-winning mass spectrometry calibration and analysis software


Cerno’s software not only enables formula determination at unit mass resolution (single or triple quad) with 100x improvement in mass accuracy (CLIPS), a capability typically reserved only for HiRes MS systems, but also improves formula ID at HiRes by 20x through the Spectral Accuracy concept (sCLIPS).  These dramatic results are enabled through the patented TrueCal™ calibration process and validated by hundreds of publications and thousands of satisfied users across the world.

For unit resolution quadrupoles:

  • 100x better mass accuracy
  • up to 99.9% Spectral Accuracy
  • Confident elemental composition determination
  • Mixture deconvolution for isotope analysis and large molecule deconvolution

For high resolution TOF, Orbitrap, FT ICR:

  • Self-calibrates peak shape without standards for exact isotope modeling
  • Eliminates 95-99% of incorrect formulas with high spectral accuracy
  • Quantitative measurements for biologics degradation analysis

Accelerate unknown compound identification

Introducing GC/ID Version 5.0
Our breakthrough vendor-agnostic automation software unlocks the true power of GC/MS.

State-of-the-art deconvolution | Vendor-agnostic software | Forward Search | Retention Index (RI) Match | Accurate Mass


MassWorks TrueCal™ calibration technology

MassWorks TrueCal™ calibration technology provides advantages for both high and low resolution instruments.

Figure shows an almost perfect match (Spectral Accuracy) between a calibrated single quad and the corresponding “True” calculated MS using the CLIPS search.

sCLIPS improves formula ID on high resolution mass spectrometers

Figure shows excellent spectral accuracy match for confident formula ID on a high resolution TOF instrument using sCLIPS search.

Proper mass spec calibration

Proper mass spec calibration also means that complex mixture deconvolution of overlapping and interfering ions is easy and provides the most accurate quantitative results.

Figure shows the accurate quantitative analysis of 7 component mixture of a C13 radio labeled pharmaceutical using a quadrupole instrument.



Figure shows the ability to detect and deconvolve modified products (glycan conjugates 0 – 10) of a large molecule intact protein (by Maldi) (see ASMS poster). This type of analysis is not possible by other means!

Powerful GC/MS Analysis Software – GC/ID™

GC/ID is the first major breakthrough in GC/MS in decades

GC/ID is a fully automated compound identification application that offers new levels of accuracy and confidence in GC/MS qualitative and semi-quantitative analysis.  Based on the new MassWorks Rx configurable platform, GC/ID offers powerful new capabilities to GC/MS including:

  • Uses the industry standard NIST search engine
  • Retention Index (RI) matching provides unsurpassed unknown ID confidence
  • Accurate mass analysis of molecular/fragment ions for confident compound ID
  • Magic Highlighter indicates at a glance the correct match by combining search, RI, and formula ID

The software that started it all… MassWorks™

Easy-to-use post acquisition software | Achieve high Mass Accuracy and high Spectral Accuracy

With over a dozen patents and 1000’s of users, the award winning MassWorks established the performance benchmark for “True” mass spec calibration.  MassWorks is a Windows based desktop software that works with most MS vendor instruments by directly reading the data files making the powerful calibration and analysis technologies available to both nominal and high resolution instruments.


NSF Case Study Presentation

New! “Accelerating GC/MS E&L Analysis with Advanced Software Tools”


NIST and Wiley MS libraries

Cerno is an authorized distributor of all NIST and Wiley MS libraries, making over 1,000,000 unique compounds available at great prices!

New! NIST23 is now available in Agilent PBM format. Contact us for a quote for new libraries or upgrades.


Cerno Bioscience GC/MS Software Accelerates Unknown Compound Identification

NEW GC/ID Version 5.0!


Featured Product

Cerno Introduces Large Molecule Analysis with SAMMI

Cerno calibration technology provides a new innovative approach to large molecule analysis for peptides, proteins, oligonucleotides,  and any multiply charged molecule.


MassWorks Version 7.0

MassWorks is still the easy-to-use post acquisition software package that utilizes Cerno’s patented TrueCal™ technology to achieve high mass accuracy and high Spectral Accuracy.


What is Spectral Accuracy

Learn how the Cerno patented TrueCal mass spec calibration works and why it is such an enabling technology for unit resolution mass spectrometers.


The concept of Spectral Accuracy for Mass Spectrometry

With the introduction of spectral accuracy, a companion concept to the better known mass accuracy, new capabilities previously thought unfeasible can now be enabled for MS.


User testimonials

  • "First let me say, we just finished the first month using GC/ID, and it works really well. Better even than we had hoped. This is really a great tool for us, so thanks for all the work you everyone at Cerno have put into it. "
    NSF InternationalNSF InternationalBenjamin Johnson
  • "We have used your MassWorks for all our publications of this year (for formula ID), we have found that in most of the cases the (mass) error is about 10 ppm" ( using LC and GC/MS single quads in 13 publications in organocatalysis in 2017-2018 all in peer reviewed journals)
    Universidad Autónoma de MadridDr. José Alemán
  • "Your software [MassWorks] continues to amaze. Your first candidate is indeed the unknown -- atranorin [LC/MS]. I'd like to get the software that works with both our Shimadzu GC-single quad and our Shimadzu LC-triple quad."
    Oberlin CollegeDr. Robert Thompson
  • "MassWorks has proven itself on our GC/MSD system for accurate mass measurements and unknown formula ID.  When applied to LC/MSD, it also worked amazingly well to provide accurate mass results for the identification or confirmation of small molecule organic compounds"
    Universidad Autónoma de MadridDr. José Alemán
  • "Starting a little bit "speechless" from our side your Presentation helped really changing our mindset, from "unbelieving" into "believer". After this Test with a sample taken from real life with real interferences my colleagues and I fully agree that MassWorks is indeed a powerful tool for advanced GC/MS analysis. We found that MassWorks is really a "must have" product for us..."
    Researcher from a large German chemical company
  • "I have tested and used the MassWorks software since the summer of 2007. The main purpose for me is using its formula ID feature to confirm the GC/MS NIST library search results for unknown chemical substance identification especially when the [NIST] search match values are similar for more than one compounds. The software is relatively simple to use and most times provides the #1 match for our testing chemicals with more than 200 compounds in a variety of chemical groups."
    User from a United States Government Environmental Lab