Please submit your challenges in an archive (*.zip) file to casmi2014@gmail.com

In the 2014 contest we are focussing on molecules originating from different sample types and differ in whether their origin is ‘natural’ or ‘synthetic’. These include:

Molecules detected in mammalian biofluids and tissues – these are molecules which have been detected in mammalian biofluids and/or tissues (challenges 1-15).

Natural products of plant, fungal or bacterial origin – these are molecules isolated and characterized from natural sources other than mammals including plants, bacteria and fungi (challenges 16-31).

Synthetic or semi-synthetic molecules – these are molecules that at the current state-of-knowledge cannot be described as natural. This may include fully synthetic molecules or derivatives of natural products (semi-synthetic molecules). To make the contest meaningful, the compounds in this category have a known human use and could conceivably be detected in the environmental (soil, water) or forensic samples. Examples may include pharmaceuticals, pesticides, fire retardants and plasticiziers (challenges 32-42).

Unknown compounds these molecules can be defined as unknown compounds. The criterion for unknown is that a SciFinder search of the structure reveals no hits. Since elucidating a completely unknown structure is a difficult task, the compounds included in this category will be unreported natural products or semi-synthetic derivatives of natural products (challenges 43-48).

There will be two categories to participate in. Each contestant can participate in one or both categories. Each contestant can choose to submit answers for all of the challenges or for a subset of challenges in each category. A single result will be reported for each category for each contestant, as was performed in previous years.

Category 1: Best Molecular Formula

Based on the MS (if available) and tandem MS (MS/MS) data, the goal is to determine the correct molecular formula using the spectral data and the additional information provided.

Category 2: Best Structure Identification

Based on the MS (if available) and tandem MS (MS/MS) data, the goal is to determine the correct molecular structure using the spectral data and the additional information provided. The additional information may include sample background, experimental factors and retention information in some cases. Whether you use this information or not is up to you!

Challenge Submission format

A plain text, tab separated file with at least two columns should be submitted for each challenge and category you wish to enter. Depending on the category for which the file applies, the first column should either contain the molecular formula or the representation of structure as the (standard) InChI or the SMILES code. The neutral compound (i.e., not the ions or adducts) should be reported. The second column should contain the score, which should be non-negative with a higher score representing a better candidate for the evaluation script to work properly. Any further information can be contained in additional columns (but will be ignored). Please do not include headers or row names. The file name should be in the format <participant>-<category>-<challenge>.txt, see here for an example from last year's submissions.

Metadata Submission format

For each participant and category, one metadata file should be submitted containing the "bibliographic" information and description of the submission. All contributions have to follow the principles of reproducible research and need to accurately describe how the results were achieved.

Please indicate whether you used automated or manual methods for your submissions in the submission metadata file, see below for details. These will be considered separately!
CASMI related formatting is excluded from the "automation" requirements.

The example submission, Challenge0, includes some results and the corresponding Metadata. Please model your submissions on this example.