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Cerno MassWorks

Cerno MassWorks for Revolutionary Mass Spectrometry Calibration and Analysis.

Version 6.0

Adding to the legacy established in previous versions, MassWorks 6.0 is still the easy-to-use post acquisition software package. MassWorks utilizes Cerno’s patented TrueCal™ technology in order to achieve high mass accuracy and high Spectral Accuracy and enable elemental composition determination on conventional mass spectrometers of unit mass resolution using the patented CLIPS formula search.

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MassWorks sCLIPS and BestScan sCLIPS now also provide high spectral accuracy through exact line-shape calibration without the need for standards. It integrates the powerful TrueCal calibration technology to obtain up to 100X improvement in mass accuracy on unit resolution systems and up to 99.9% spectral accuracy on both high and unit resolution systems in a fast and versatile MS application software package. By mass accuracy with Spectral Accuracy, Cerno methodologies can provide significant improvements to all types of MS data, both high and low resolution.

  • High mass accuracy on quadrupole GC or LC/MS (up to 0.005Da)
  • Improved Spectral Accuracy on all systems (up to 99.9%)
  • Elemental composition determination on quadrupoles
  • Eliminating up to 95-99% of incorrect elemental compositions on high resolution MS
  • Accurate isotope fine structure analysis on ultra-high resolution MS
  • Direct and accurate analysis of unresolved mixtures, e.g.,isotope labeling and biologics modification

MassWorks now includes sCLIPS and Best Scan sCLIPS, for improving formula ID on high resolution MS. In addition , and CLIPS, for enabling formula ID on unit resolution GC or LC/MS single or triple quadrupoles.

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

For unit resolution quadrupoles:

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

Spectral Accuracy

Spectral Accuracy is a measure of the similarity between the measured isotope pattern (ion’s mass spectrum) and the ion’s true mass spectrum sampled in the profile or continuum mode. Without proper line-shape calibration, Spectral Accuracy values are of limited use in identifying the unknown formula. An ion’s isotope pattern is unique for every unique formula and significantly richer in information than the measurement of a single peak position, as with accurate mass measurements.

An ion’s mass spectrum is composed of many peaks each with unique relative intensities based on their isotopic abundances, and unique relative mass positions based upon the mass of each isotope. Spectral Accuracy is a measure of the similarity between the measured spectra (the entire isotope envelope) against that of the true spectrum which can be accurately calculated.

However, since the line-shape of the measured spectrum is unknown, measures of Spectral Accuracy are generally not high enough to provide a unique formula ID.  Cerno’s MassWorks™ software elegantly addresses this problem by not only calibrating the mass position of the peak, but by also calibrating the line-shape to a mathematically defined function. This allows to make extremely accurate comparisons between measured and true spectra with Spectral Accuracy values capable of uniquely identifying an unknown ion formula.

Once the line-shape is properly calibrated, not only can one perform more accurate formula search, but it becomes possible to accurately deconvolve complex mixtures. Overlapping interferences and background are perhaps one of the most perplexing problems in mass spectrometry. Since the mass spectra can now be accurately calibrated and quantitatively compared with true mass spectra, mixture deconvolution, including direct quantitation of isotope-labeled compound mixtures, becomes trivial.


CLIPS (Calibrated Line-shape Isotope Profile Search) is a revolutionary way to attain fast and reliable elemental composition determination. Elemental composition is determined using the accurate mass information to identify a list of formula candidates. But even with very high mass accuracy, the list of formula candidates can make unambiguous formula determination difficult.

Unlike approaches that use only mass accuracy for this purpose, CLIPS adds another accurate dimension to formula ID by matching the full isotope envelope of the unknown to the true mass spectrum of a candidate ion. In the past, this has not been possible due to the unknown line shape in mass spectrometry. The TrueCal™ implemented in the MassWorks™ not only calibrates these instruments to accurate mass, it also calibrates the actual instrument line shape to a known mathematical function. This allows for the accurate calculation of the theoretical isotope profile for each formula candidate using the same line shape as the calibrated line shape and thus its true mass spectrum.

The CLIPS algorithm then matches each formula candidate to the unknown and calculates a highly reliable statistic with typically less than 1% relative spectral error, a level of profile accuracy called Spectral Accuracy necessary to differentiate candidate formulas and arrive at unambiguous formula determination, even on a unit mass resolution system such as a single quadrupole MS.

The CLIPS algorithm first uses conventional formula determination based on mass accuracy and various formula search criteria (e.g. mass error or tolerance, elements, DBE, electron state, and charge). Once this list is calculated, CLIPS will then calculate the true mass spectrum for each formula and match it over the defined mass range to the unknown ion. The “Spectral Accuracy” of the match will then be generated which is calculated as follows: (1-RMSE)*100. (RMSE: root mean squared error expressed as a fraction of the overall MS signal in the mass range). Thus, a RMSE of .005 would indicate that the fit spectral error is .005 or .5%; this translates to an easily interpretable Spectral Accuracy value of 99.5%.

Ideal for unit resolution instruments (e.g. single quad GC/MS, LC/MS)

  • 100x improvement in mass accuracy from 0.x to 0.00x Da
  • Greater than 99% Spectral Accuracy achievable on chromatographic time scale
  • Accurate formula ID enabled even at the unit resolution price
  • Powerful mixture analysis with un-resolved MS signals

Best Scan sCLIPS™

In conventional sCLIPS, typically the averaged MS across a chromatographic peak is used to correct the instrument line-shape and enable exact isotope modeling for Spectral Accuracy evaluation of various possible elemental compositions. With ultra-high resolution MS at ≥ 240,000 resolving power, the observed fine isotopes can vary systematically from scan to scan, depending on the ion population and the associated space charge effects.

Best Scan sCLIPS goes beyond the conventional sCLIPS to evaluate the attainable Spectral Accuracy for each and every scan while searching for possible elemental compositions. The scan with the best Spectral Accuracy (oftentimes not at the chromatographic peak apex) will be selected and utilized for accurate elemental composition determination.

  • Exact line-shape calibration without standards
  • Comparing calibrated spectra to theoretical with up to 99.0% Spectral Accuracy
  • Automatic selection of best Spectral Accuracy scan
  • Unknown ID: Ultra HiRes Orbitrap or FT ICR MS
  • Relative quantitation of known ion mixtures: any HiRes including TOF or Orbitrap


sCLIPS™ (self Calibrating Line-shape Isotope Profile Search) enables users of accurate mass instruments including TOF, high resolution quadrupoles, Orbitrap, magnetic sector, and FT-ICR MS to dramatically improve formula ID through Spectral Accuracy without the need to run calibration standards.  The patented sCLIPS approach utilizes the fully resolved monoisotopic peak from high resolution instruments to create a line-shape TrueCal™ calibration that is applied to the entire isotope profile of the ion of interest.

This enables exact isotope modeling when comparing the MS response of an unknown ion against the true mass spectra (theoretically calculated responses) for all possible candidate formulas and allows spectral differences as small as 0.1% to be measured, leading to formula ID. One of the benefits of the approach is that it requires no known calibration ions, and instead utilizes the fully resolved monoisotopic peak of the unknown ion itself for the sCLIPS line-shape calibration.

The flow diagram below illustrates the steps performed with sCLIPS. For sCLIPS to perform properly, the monoisotopic peak must be fully resolved from the A+1 isotope peak, a level of resolving power easily achieved by higher resolution systems for singly charged small molecule compounds (m/z < 1,000). It is important to note that sCLIPS does not calibrate for or improve mass accuracy, which is required by CLIPS on low resolution MS. It only calibrates the line-shape while preserving the same (high) mass accuracy of the high resolution MS. However, the line-shape calibration is near perfect since the monoisotopic peak is as close as practical in mass and measurement time to the other isotope peaks.

Ideal for high resolution instruments (e.g. TOF, Orbitrap, FT-ICR)

  • No calibration compounds necessary
  • The mono-isotopic peak of unknown as the TrueCal standard
  • Unique, patented self-calibration
  • Mathematically exact isotope modeling
  • ≥ 99% Spectral Accuracy achievable on well designed and operated systems
  • Going beyond mass accuracy alone for formula ID
  • Capable of eliminating up to 95-99% of incorrect formulas
  • Powerful mixture analysis with un-resolved MS signals

More information:

For more information on Cerno MassWorks (incl. instruction video’s, webinars, etc.), visit our online library.

MassWorks V6.0 Brochure:

For more information on Cerno Bioscience, click here.