These challenges are used in Category 2, 3 and 4.

Challenges 46-243

These challenges are all natural products, Challenges 46-131 are measured in negative mode and Challenges 132-243 in positive mode.

Update 22/05/2017: We have improved challenges 71, 89, 105, 106 and 144.
Update 09/07/2017: We have fixed the intensities in the TSV archive for challenges 046-243. The intensities in the MGF files were correct and are unaffected.

Challenge data

challenges-046-243-msms-tsv.zip
challenges-046-243-msms-mgf.zip

For Category 4, the candidate lists for Challenges 46-243 are available as InChI or SMILES, either with all stereoisomers retrieved from PubChem ("full"), or pre-filtered with an arbitrary stereo configuration per 2D structure ("nonredundant"). If your method gives identical scores to different stereo isomers, the pre-filtered candidates will be more efficient and result in the same evaluation.

	InChI	SMILES
full	zip	zip
nonredundant	zip	zip

Since the ion species are not specified for these Challenges, candidates were retrieved from PubChem using an accurate mass search (6 ppm deviation) for compounds assuming the adducts [M+H]+, [M+Na]+, [M+NH4]+ in positive mode, and [M-H]-, [M+Cl]- and [M+COO]- (i.e. the formic acid adduct [M+FA-H]-) in negative mode.

The candidates were retrieved as InChI structures from PubChem (mirror dated 2017-02-03) using MetFrag 2.4.2 and converted to SMILES with OpenBabel 2.4.1 .

Analytical conditions

Challenge compounds were acquired on a Waters HDMS SYNAPT quadrupole/time-of-flight mass spectrometer using electrospray ionization in MS^E mode, with the ultra performance liquid chromatography (UPLC) column connected online to a photodiode array detector and then to the MS detector. Typical mass accuracy was <6 ppm in both positive and negative ionization modes, however, some low intensity ions are outside of these mass error limits. The collision energy was set to 4 eV for low-energy function and to 10–30 eV ramp for the high-energy function in the positive ion mode (15–35 eV in the negative ion mode). Scan time for each function was set to 0.25 s.

Chromatographic Method:

A 100×2.1-mm i.d., 1.7-μm UPLC BEH C18 column (Waters) was used for chromatographic separation. The mobile phase consisted of 0.1% formic acid in acetonitrile: water [5:95, (vol/vol); phase A] and 0.1% formic acid (vol/vol) in acetonitrile (phase B).

The linear gradient was from 100 to 72% phase A over 22 min, from 72 to 0% phase A over 14 min, then held at 100% phase B for further 2min; and then returned to the initial conditions (100% phase A) in 0.5min and conditioning at 100% phase A for 1.5min. A divert valve (Rheodyne) excluded 1.0 and 38 min from the injection.