CENAPT - University of Illinois at Chicago

✍ The Lockdown Mass Spec Challenge (extended)

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Due to overwhelming interest, we are releasing 4 additional challenges. Due to their late release, these additional challenges will not be counted towards rankings but participants trying new ID methods may find them useful as they mostly contain negative ion data which are scarcely represented in the original set.

What a better way to spend The Lockdown than to solve MS-MS spectra? The UIC Botanical Center and the CENAPT Center are pleased to organize The Lockdown Mass Spec Challenge. The Challenge follows the model used in the recent rounds of the CASMI contests. We are providing a set of 16 MS and MS-MS spectra and are asking participants to deduce the structure of compounds based on the provided data. The compounds are all derived from plants and include both known and unknown compounds. The unknown compounds are either unreported natural products or semi-synthetic analogs of known natural products. Metadata including origins of the compounds and chromatographic data are also provided. Participants can use any approach to arrive at the structures.

Follow-up wet sample challenge

We are considering organizing a ring trial in which participants will be provided a wet sample consisting of moderately complex mixture of natural products (25-35 compounds) and asked to identify compounds in the mixture. The objective of this trial would be to evaluate the current approaches for identification of natural products using mass spectrometry. If interested, please send a short email notice indicating your intent to participate as well as your willingness to contribute to the cost of shipping the sample. This notice is not binding but would help the organizers estimate the cost of running the trial, determine the workload and estimate the amount of sample necessary. Please, send the notice of interest to Dr. Dejan Nikolic at dnikol1@uic.edu.

Submission format

Because in real metabolomics studies only one compound per spectrum is reported, we are asking participants to submit only a single solution per challenge. The results should be submitted as a single, plain text, tab separated file with at least two columns. The first column should contain the number of the challenge, the second the representation of the structure as the (standard) InChI-Key and the third column should contain the SMILES code*. Do not include headers or row names. Any row that contain invalid or empty entries will not be accounted for. Report the small molecules themselves, not the adduct species like [M+H]+. Molecules that you consider to be charged in the natural state (for example, quaternary amines) should be reported as such. Along with solutions file, submit a plain text file with name(s) and institutional affiliation of the participant(s). You do not need to describe the method used to arrive at solutions, although you are welcome to do so. Please, label the result file as participant_name.tsv and the text file containing your names and affiliations participant_name.txt (replacing participant_name by your team name). For the purpose of reporting results, you have an option to remain anonymous. Please, indicate so in your submission (in your txt file). Performance of anonymous entries will still be posted under “Anonymous” designation. In addition, by remaining anonymous you will forfeit the right to participate in writing of a possible future publication that may arise from this initiative. Please, submit your entries via email to both Dr. Jonathan Bisson (bjo@uic.edu) and Dr. Dejan Nikolic (dnikol1@uic.edu).

If you need help creating a TSV file: - LibreOffice - Microsoft Office

  • We ask for both to make sure we are not hitting a SMILES or InChIKey implementation discrepancy.

Important deadlines

The deadline for submission is now June 10th (if you submitted already, you can resubmit to replace or add another solution up to 3). If you didn’t submit yet, you can submit up to 2 submissions if you want to assess different approaches. Solutions and results will be posted by mid June. The participant who correctly solves the highest numbers of challenges will be declared winner.

Challenge information

All challenge data were acquired on a Waters SYNAPT quadrupole/time-of-flight mass spectrometer using electrospray ionization. Typical mass accuracy is ≤8 ppm in the MS mode and ~15 ppm or 2.0 mDa in the MS/MS mode. Some low intensity ions may have accuracies outside of these limits. Most compounds were analyzed using a generic LC method (Method A). Challenges analyzed with different methods are indicated; the corresponding methods are listed below. The flow rate was always 0.2 mL/min. Challenge 13 is a legacy spectrum for which no metadata data can be provided other than that the spectrum was acquired on a qTOF instrument. Details (including some background information, mode, collision energies, method and retention times) are given in the summary below.

Ch. No Description Method RT ESI Mode Collision energy (eV)
1 Identified in Boraginaceae B 11.4 Positive 25
2 A semisynthetic analog of Ch. 1 B 10.5 Positive 30
3 Plant-derived A 11.7 Positive 25
4 Common in foods such as wine, chocolate, peanuts, fruits A 5.0 Positive 6-50 ramp
5 Plant-derived A 11.3 Positive 25
6 From licorice A 21.4 Positive 6-50 ramp
7 Common in Leguminosae A 14.7 Negative 25
8 Common in Leguminosae Infusion - Positive 25
9 Rare plant-derived compound A 8.7 Positive 15
10 Common in Leguminosae A 15.4 Positive 25
11 Identified in licorice A 21.3 Positive 6-50 ramp
12 Plant derived A 14.4 Positive 25
13 Plant-derived Legacy N/A Positive N/A
14 Unreported compound identified in licorice A 19.9 Positive 25
15 Unreported compound identified in Ranunculaceae 6-36%B 30 min 9.8 Positive 15
16 A semisynthetic analog of a common plant compound A 5.0 Positive 15
17 A compound from mangosteen fruit 50-90%B 15min 12.4 Negative 30
18 Endogenous A 2.0 Negative 15
19 Common in foods such as wine, chocolate, fruits A 8.9 Negative 15
20 Plant derived A 12.6 Positive 6-50 ramp

Chromatographic conditions: Method A: YMC AQ 2.0x100 mm, 3µm; 10-95%MeCN/0.1%formic acid over 30 min

Method B: YMC AQ 2.0x100 mm, 3µm; 5-40%MeCN/0.1%formic acid over 30 min

Challenge Data