Easy-to-use interface for routine analysis and comprehensive results review
Integrated user interface
All functionalities in a single interface (submission, results evaluation, reporting, library management, administration).
+ Click to see large screenshot
Workflows to suit users’ level of expertise
While LC-MS users have variable levels of knowledge in the technology and requirements in the interpretation of data, SmileMS provides the right workflow for each of them. From a simple two-step approach designed for novice LC-MS users and routine technicians to a more in-depth evaluation process for expert users (senior technicians, clinical laboratory directors, etc.), SmileMS meets both routine and research workflows thanks to a dynamic and easy-to-use interface.
Two-step workflow for routine technicians
After login to SmileMS, user reaches the analysis list page. The 2-step procedure consists of:
- Submit new analysis + Click to see large screenshot
- Generate PDF report from the analysis list + Click to see an example of a PDF Analysis Report
Highly interactive interface for result review and in-depth analysis
The result is represented as a list of qualified molecules, identified on a chromatogram.Individual spectra interpretations supporting the identifications are aggregated into chemical compounds. Multiple results open in separate tabs.
In the chromatogram, the list of molecules and the spectrum viewer are dynamically linked.
- The identified molecules are listed and sorted by confidence level
- The molecules are labeled in an interactive chromatogram
- The spectra supporting the identification of a molecule are aggregated in the table
- Individual matching spectra are made available in the spectrum viewer and displayed in a head-to-tail representation of reference and experimental spectra for easy evaluation
- Access to spectra annotation and alternative, lower quality matches (best match, second rank, third, etc.)
Analysis workspace for organizing results and analyses
Each analysis appears in the Analysis list table with descriptive information (date, sample name, user,etc.) and one-click PDF report. Users can decide to resubmit previously analyzed samples (e.g. under different conditions to search against other libraries, with alternative filtering criteria, etc.) and easily manage analyses - hide, unhide, sort, search.
Efficient spectra library management
Depending on their defined user rights, a user can add new
libraries, edit spectrum annotation, visualize compounds and associated spectra, add/delete spectra to/from libraries, with a single mouse click.
Outstanding compound identification with highest levels of confidence
SmileMS is designed to screen a sample containing unknown molecules against one or more MSMS spectra libraries. Experimental fragmentation spectra obtained from a sample of interest are compared with those stored in a library of target molecules.
Although algorithms exist elsewhere on the market, their performances have limitations when it comes to analyzing experimental spectra that slightly or clearly differ from those of available libraries, which is the case in LC-MSMS. The current widely-used algorithms suffer when a major signal is absent or if the intensities of compared spectra do not match.
SmileMS considers intensity ranks and models a probabilistic cross-correlation algorithm that is highly robust against intensity variability and locally missing signals. It works best when very similar conditions are used to generate experimental and library spectra; it is also very efficient when collision energies vary or even if instruments differ between the library and the experimental data. For example, a user can comfortably search the NIST MSMS library with an AB SCIEX QTRAP® instrument, which is poorly represented in this library.
The imbedded X-rank algorithm
, developed by GeneBio, has demonstrated superior performances when compared to existing algorithms. It highlights better specificity and sensitivity when searching data against libraries originating both from similar and differing instrumentation. More information about X-rank can be found in Analytical Chem. 81, 7604 (2009)
Note: ROC curve showing the superior performances of SmileMS (in red) vs NIST MS Search (blue), when searching NIST MSMS against itself, in a leave-one out manner (all spectra are searched against the whole library except themselves).
Easy interpretation eliminating false positive identification
Score values range between 0 and 1. A high value indicates a high probability of being correct. There is just one value to look at. SmileMS not only provides confidence levels in its score: for each spectrum it also maximizes the discrimination between the best compound (may be represented with more than one spectrum) and less good interpretations. Often only one molecule reaches score threshold, facilitating the exclusion of false positives.
- Diazepam is identified
- Four spectra supporting the diazepam identification
Filters for identification of metabolites and other unknown compounds
SmileMS uses m/z and retention time filters only as a post-processing filter. Deactivating the filters in a result allows for recovering molecules that are showing apparent wrong masses, such as due to adducts, alternative charge states and wrongly assigned precursor mass. It also allows identification of metabolites not available in libraries, which spectra resemble the main compounds but have different molecular mass.
Take advantage of accurate mass
SmileMS considers actual m/z values when comparing library and experimental spectra. In this respect it does not have to reduce the mass accuracy of the instrumentation to 1 Da bins. When searching high mass accuracy MSMS spectra against a library of similar precision (e.g. with fragments annotated at 4 decimals), the MSMS search precision can be as low as 0.001 Da, greatly enhancing the specificity of high mass precision MSMS acquisition.
Single software for multiple MS instruments, libraries and application fields
Compatibility with LC-MSMS instruments
SmileMS can be used as a single entry point to analyse LC-MSMS runs from multiple instruments. In addition to the cross-instrument capabilities of i(from the same vendor or from different ones), users can rely on a single graphical interface to convert and process raw data from major instrument manufacturers.
Note: Non-exhaustive list of supported MS instruments and raw files generating full scans of product ion scans experiments. In addition, peaklist formats such as .mgf, .mzXML and .sdf are also accepted.
Multi-library capabilities increases identification results
SmileMS can search both low and high mass accuracy instruments and libraries. Users can search on various libraries simultaneously, including privately built ones.
Searching libraries originating from different MS instruments (including fragmentation mode) allows searches for molecules that are not present in the most similar library. For example:
- A SmileMS user using a Thermo LTQ (or LXQ) and an AB Sciex QTRAP® can search NIST MSMS and AB Sciex LC/MS/MS Forensic libraries with both instruments, therefore taking advantage of the complementary molecular coverage of the two libraries. This would allow the user to search the Thermo LTQ data on the AB Sciex Forensic library and identify compounds absent from NIST MSMS.
- Searching AB SCIEX QTRAP® data on an AB SCIEX Forensic LC-MSMS and NIST MSMS library allows for searching compounds outside of the Forensic interest as covered by the Forensic library.
Large range of application fields
SmileMS is successfully used in Clinical and Forensic Toxicology, as well as Food Testing. Its extension to other fields such as Laboratory Medicine, Environmental, Pharmaceutical and Metabolomics is also possible.
Flexible user access through standalone or network mode
SmileMS is intrinsically built with client-server architecture so that it can be installed as a standalone program on any PC or on a server for network access by multiple users. Remote access is therefore possible via a standard Web browser; this gives users the freedom to launch analyses and review results from other locations (e.g. office, home, etc.).
SmileMS incorporates its own queuing system for automated data submission management, making possible multi-sample submission in parallel.
The raw data processing environment uses the open source Proteowizard
tool to extract peaklists from various vendors' raw data files. This software is packaged in an installer, made available for free, to facilitate its installation.
Automation with “SmileMS Submission Module” for greater productivity
This software module connects seamlessly with Thermo Scientific Xcalibur and Bruker Data Analysis software to perform data submission to SmileMS. Once the processing method is configured in Xcalibur or Data Analysis, samples are automatically submitted to SmileMS at the end of an acquisition. No more manual file uploads are required and productivity in data analysis is significantly improved.