MassWorks is a software for both low resolution (quadrupole) MS as well as high resolution MS (TOF).
Normally most people are looking att mass accuracy but in combination with spectral accuracy you can even get the right formula id from a low resolution mass spectrum.
Low Resolution (Quadrupole) - CLIPS
CLIPS (Calibrated Line-shape Isotope Profile Search) is an entirely new and 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 Cerno software product including 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 is then generated which is calculated as follows:
where RMSE is the 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%.
High Resolution (TOF) - sCLIPS
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, but 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.
Ultra High Resolution (OrbiTrap) - Best 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.
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.
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