These challenges are used in Category 1, 2 and 3.

Challenges 1-45

Most of these challenges are plant-derived compounds and a few that are endogenous to humans. Note that some of these compounds may be charged in their natural state! Due to often unique distribution of some of the compounds, only limited metadata on the compounds’ origin are provided.

There are a few "unknown" compounds, i.e. structure search in e.g. PubChem or the SciFinder database results in no hits (as of 03/2017). The compounds are either unreported natural products (NP) or synthetic analogs of known natural products. The main idea behind inclusion of this subset is to test the ability of current approaches to identify structural analogs of known natural products. Thus, the structural modifications of known compounds are those that either occur or could conceivably occur in nature.

Update 20170522: We have fixed MS1 data for challenges 29 and 42

Update 20170908: We have fixed MS2 data for challenge 15, but due to the late timing will not count Challenge-15 in the evaluation.

Challenge data

challenges-001-045-ms-tsv.zip
challenges-001-045-ms-mgf.zip

challenges-001-045-msms-tsv.zip
challenges-001-045-msms-mgf.zip

The updated challenge-15 files are also available individually as TXT and MGF.

Analytical conditions

All challenge data were acquired on a Waters SYNAPT quadrupole/time-of-flight mass spectrometer using electrospray ionization. Typical mass accuracy is ≤10 ppm in the MS mode and ~10 ppm or 2.0 mDa in the MS/MS mode. Some low intensity ions may have accuracies outside of these limits. Most compounds were analysed using a generic LC method (Method A). Challenges analysed with different methods are indicated; the corresponding methods are listed below. The flow rate was always 0.2 mL/min. Challenge 28 was measured via direct infusion. Details (including some background information, mode, collision energies, method and retention times) are given in the summary below.

Challenge 1-45 information:

ChalNo	Description	Method	RT	ESI.Mode	CollisionEnergy.eV.	MS_files	MSMS_files
1	Plant-derived	A	13.80	Pos	15	challenge-001-ms.txt	challenge-001-msms.txt
2	Isolated from the Fabaceae family	A	19.30	Pos	20	challenge-002-ms.txt	challenge-002-msms.txt
3	Plant-derived	B	13.30	Pos	15	challenge-003-ms.txt	challenge-003-msms.txt
4	Common natural product	A	12.70	Pos	25	challenge-004-ms.txt	challenge-004-msms.txt
5	Common natural product	A	11.90	Pos	25	challenge-005-ms.txt	challenge-005-msms.txt
6	Common natural product	A	13.10	Pos	30	challenge-006-ms.txt	challenge-006-msms.txt
7	Common natural product	A	14.10	Pos	30	challenge-007-ms.txt	challenge-007-msms.txt
8	Plant-derived	A	13.60	Pos	20	challenge-008-ms.txt	challenge-008-msms.txt
9	Isolated from the Fabaceae family	A	18.90	Neg	25	challenge-009-ms.txt	challenge-009-msms.txt
10	Plant-derived	A	1.80	Pos	15	challenge-010-ms.txt	challenge-010-msms.txt
11	Found in several plant species	C	9.84	Pos	6-50 ramp	challenge-011-ms.txt	challenge-011-msms.txt
12	Plant-derived	A	5.80	Pos	25	challenge-012-ms.txt	challenge-012-msms.txt
13	Relatively common NP isolated from many plants	A	12.40	Pos	25	challenge-013-ms.txt	challenge-013-msms.txt
14	Relatively common plant-derived compound	A	12.20	Neg	25	challenge-014-ms.txt	challenge-014-msms.txt
15	Relatively common plant-derived compound	A	13.60	Neg	25	challenge-015-ms.txt	challenge-015-msms.txt
16	Isolated from hops	A	14.90	Pos	15	challenge-016-ms.txt	challenge-016-msms.txt
17	Isolated from multiple plant species	D	5.10	Neg	15	challenge-017-ms.txt	challenge-017-msms.txt
18	Isolated from Ferula species	E	11.60	Pos	15	challenge-018-ms.txt	challenge-018-msms.txt
19	Found in human fluids	A	1.80	Pos	15	challenge-019-ms.txt	challenge-019-msms.txt
20	Plant-derived	A	5.80	Pos	25	challenge-020-ms.txt	challenge-020-msms.txt
21	Identified in the Ranunculaceae family	A	3.10	Pos	15	challenge-021-ms.txt	challenge-021-msms.txt
22	Isolated from Ferula species	A	25.10	Pos	6-50 ramp	challenge-022-ms.txt	challenge-022-msms.txt
23	Isolated from several plants	F	9.70	Pos	15	challenge-023-ms.txt	challenge-023-msms.txt
24	Identified in plants and human tissues	A	1.80	Pos	15	challenge-024-ms.txt	challenge-024-msms.txt
25	Product of endogenous metabolism	A	1.80	Neg	15	challenge-025-ms.txt	challenge-025-msms.txt
26	Isolated from multiple plant species	G	20.30	Neg	25	challenge-026-ms.txt	challenge-026-msms.txt
27	Isolated from Crotalaria species	A	3.80	Pos	25	challenge-027-ms.txt	challenge-027-msms.txt
28	Identified in various food preparations; artefact of sample processing	Infusion	-	Pos	15	challenge-028-ms.txt	challenge-028-msms.txt
29	Common constituent of fruit and vegetables	A	9.20	Pos	15	challenge-029-ms.txt	challenge-029-msms.txt
30	Relatively common NP isolated from many plants	A	12.10	Pos	6-50 ramp	challenge-030-ms.txt	challenge-030-msms.txt
31	Plant-derived	H	12.30	Neg	30	challenge-031-ms.txt	challenge-031-msms.txt
32	Common plant-derived NP	A	14.10	Pos	15	challenge-032-ms.txt	challenge-032-msms.txt
33	Rare plant-derived NP	A	7.30	Pos	15	challenge-033-ms.txt	challenge-033-msms.txt
34	Rare plant-derived NP	A	8.70	Pos	15	challenge-034-ms.txt	challenge-034-msms.txt
35	Isolated from Apiaceae family. Extensive in-source fragmentation	A	23.40	Pos	15	challenge-035-ms.txt	challenge-035-msms.txt
36	Plant-derived	C	15.30	Pos	25	challenge-036-ms.txt	challenge-036-msms.txt
37	Isolated from Ferula species	A	22.80	Pos	15	challenge-037-ms.txt	challenge-037-msms.txt
38	Plant-derived	A	19.40	Neg	25	challenge-038-ms.txt	challenge-038-msms.txt
39	Identified in legumes	A	18.10	Neg	15	challenge-039-ms.txt	challenge-039-msms.txt
40	Common constituent of fruit and vegetables	A	8.80	Neg	15	challenge-040-ms.txt	challenge-040-msms.txt
41	Plant-derived	C	17.60	Pos	25	challenge-041-ms.txt	challenge-041-msms.txt
42	NP or synthetic analog	A	1.80	Pos	15	challenge-042-ms.txt	challenge-042-msms.txt
43	NP or synthetic analog	A	10.50	Pos	15	challenge-043-ms.txt	challenge-043-msms.txt
44	NP or synthetic analog	A	1.80	Pos	15	challenge-044-ms.txt	challenge-044-msms.txt
45	NP or synthetic analog	F	2.80	Pos	15	challenge-045-ms.txt	challenge-045-msms.txt

This table is also available as CSV download.

Chromatographic Methods:

Method	Description
Method A	YMC AQ 2.0x100 mm, 3µm; 10-95%MeCN/0.1%formic acid over 30 min
Method B	Hypersil GOLD 2.0x150mm; 18-62%MeCN/0.1% formic acid over 12 min
Method C	Hypersil GOLD 2.0x150mm; 6-65% MeCN/0.1% formic acid over 30 min
Method D	XBridge 2.0x50mm; 20-80%MeCN/0.1% formic acid over 10 min
Method E	Hypersil GOLD 2.0 x150mm; 50-95%MeCN/0.1% formic acid over 10 min
Method F	Hypersil GOLD 2.0x150mm; 6-36%MeCN/0.1% formic acid over 30 min
Method G	XBridge 2.0 x 50mm; 10-95%MeCN/0.1% formic acid over 30 min
Method H	YMC AQ 2.0x100m; 50-95%MeCN/0.1% formic acid over 15 min