Some of the smaller subformulas generated by our Rational Numbers Excel Add-In correspond to one or just a few substructures. We demonstrated previously how substructure searching can be performed on the Pubchem Compound database (Subfragments and Substructures). However, this requires drawing the substructures, which is somewhat time-consuming, and some of the very common substructures will generate over one million hits because the entire Pubchem database must be searched. We are now beta testing a new worksheet that makes it very easy to do substructure searches in Pubchem Compound - no substructures need to be drawn. This worksheet also uses Pubchem's new "Search Within A Search" capability to limit the search space to a single molecular formula.
Please watch our "Search Within a Search" video on YouTube.
"Non-targeted screening of trace organic contaminants in surface waters by a multi-tool approach based on combinatorial analysis of tandem mass spectra and open access databases. (https://doi.org/10.1016/j.talanta.2021.122293)
Emmauel Eysseric, Francis Beaudry, Christian Gagnon and Pedro A. Segura published a study in Talanta in March 2021 describing how three NTS tools were combined and used to detect and identify unknown contaminants at ultra-trace levels in surface waters in real samples. Two of the tools are based on combinatorial fragmentation databases: MetFrag and MathSpec's Similar Partition Searching algorithm (SPS). The third tool, the Global Natural Products Social Networking (GNPS), is an ensemble of empirical databases. These three NTS tools were applied to the analysis of real samples from a local river. A total of 253 contaminants were identified by combining all three tools: 209 were assigned a probable structure and 44 were confirmed using reference standards. The two major classes of contaminants observed were pharmaceuticals and consumer product additives.
Based on the tabulated results in the supplemental spreadsheet, SPS identified the most compounds. The authors reported that SPS is an easy tool to use and integrates well with the Microsoft Access database.
"Mass Spectrometry by the Numbers, Identifying Small Molecules from Accurate-Mass Fragmentation Data, 2nd edition" 11-May-2020
Dan Sweeney's updated book on mass spectral identification was recently published. This book describes the theory of "partitioning" and how this approach was implemented as a simple Excel Add-In. This book will be very useful to anyone who is identifying small molecules using accurate-mass fragmentation. This book can be purchased on your local Amazon website: "Mass Spectrometry by the Numbers, 2nd edition." The e-pub version is always free if you have Kindle Unlimited. Kindle owners with Amazon Prime can also borrow the book at no cost through the Kindle Owners' Lending Library.
"Nontargeted Screening of Water Samples Using Data-Dependent Acquisition with Similar Partition Searching" 01-May-2020 (DOI: 10.1021/jasms.0c00031)
MathSpec's Dan Sweeney was honored to be a co-author on a recent publication in JASMS with co-authors Imma Ferrer, E. Michael Thurman, and Jerry A. Zweigenbaum. This paper describes a rapid screening method for the detection of nontargeted compounds in surface water samples that was developed using accurate-mass fragmentation data acquired by data-dependent acquisition. Eighteen surface water samples from rivers, reservoirs, and effluents from waste- water treatment plants were analyzed, generating 41625 MS-MS spectra in about 14 h. The raw data were then converted into two generic formats using the open-access program MSConvert. A combinatorial approach, similar partition searching (SPS), was then used to putatively identify analytes from the accurate mass of each analyte (adjusted for the adduct mass) and the corresponding MS-MS spectra were obtained. In this approach, the structures of about 250000 common compounds, stored in a large database as mathematical partitions of their exact mass, were compared directly to each MS-MS spectrum.
"Similar Partition Searching is now available for rapid screening of very complex samples." 15-Jul-2019
MathSpec has now launched Similar Partition Searching on Amazon Web Services. For a very reasonable cost, users can rapidly screen very complex samples. This is especially useful for food safety and environmental applications, but it can also be used with our Excel Add-in to decentralize data analysis in central service laboratories. A brief description is attached here: "Partition Searching"
"MathSpec at ASMS 2019 in Atlanta" 03-Jun-2019
MathSpec's Dan Sweeney was honored to be a co-author on a poster presented at ASMS in Atlanta with co-authors Imma Ferrer, E. Michael Thurman, and Jerry A. Zweigenbaum. This poster illustrated the critical importance of optimizing DDA (data dependent analysis) parameters prior to analyzing samples. By optimizing the mass spectral parameters, taking into account the downstream Agilent Decision Engine and Partition Searching operations, twenty aqueous environmental samples were screened very rapidly. Here a huge dataset of over 37000 MS/MS spectra was obtained and analyzed. This approach is especially useful for food safety and environmental applications. The poster is attached here; it eventually will also be available in the ASMS 2019 Proceedings: "Rapid Non-Targeted Screening of Aqueous Environmental Samples Using Auto MS/MS"
Similar Partition Searching 08-Oct-2017
Rational Numbers Search was moved from our own MathSpec server to Amazon AWS. This increased CPU power now makes in possible to search every MS/MS spectrum in a chromatogram. Contact us now for your free two-week trial. To see exactly how Similar Partition Searching (SPS) works, please view our short MathSpec YouTube Video on SPS.
Similar Partition Searching 4-28-2016
Rational Numbers Search has been moved from our own MathSpec server to Amazon AWS. This increased CPU power has allowed us to also add simultaneous searching for similar compounds.
New Capabilities Added 02-19-2016
Two new worksheets have been added to the Excel Add-In.
The first worksheet is a summary of all of the elemental compositions of all assigned fragments. With built-in filters for each parameter, this makes it much easier to sort through the results that have a large number of possible molecular formulas.
The second worksheet is a high resolution isotope calculator that tabulates the expected masses of the first and second isotopes. The isotopic patterns of the first and second isotopes are then plotted in color in a normal distribution based on the selected resolution setting. (example here)
Excel® 2016 11-25-2015
The Excel Add-In is compatible with Excel 2016. Use the installation video (MathSpec YouTube) for Excel 2013.
SubFragment Color Change 11-9-2015
Based on feedback, the color of the fourth subfragment has been changed to a shade of purple, making it easier to distinguish from the other cells.