Appendix 1: The MSP File Format and package support

Name: unknown Num Peaks: 2 85.345 100; 76.321 50;

Listing S1: Example for the basic NIST format.

Name: 1-Methylhistidine Synon: (2S)-2-amino-3-(1-methyl-1H-imidazol-4-yl)propanoic acid SYNON: $:00in-source DB#: HMDB0000001_c_ms_1469 InChIKey: BRMWTNUJHUMWMS-LURJTMIESA-N Instrument_type: GC-MS Retention_index: 1807.71 Formula: C7H11N3O2 MW: 169 ExactMass: 169.0851 Comments: “column=5%-phenyl-95%-dimethylpolysiloxane capillary column” “derivatization type=2 TMS” “derivatization formula=C13H27N3O2Si2” “derivative mw=313.544” “retention index=1807.71” “retention index type=based on 9 n-alkanes (C10–C36)” “instrument type=GC-MS” “chromatography type=GC” “cas number=332-80-9” “molecular formula=C7H11N3O2” “total exact mass=169.085126592” “InChIKey=BRMWTNUJHUMWMS-LURJTMIESA-N” Num Peaks: 10 70 0.014; 71 0.007; 72 0.02; 76 0.008; 77 0.008; 78 0.002; 79 0.003; 80 0.005; 81 0.108; 82 0.017;

NAME: Aspartame; LC-ESI-ITFT; MS2; CE PRECURSORMZ: 295.128848 PRECURSORTYPE: [M+H]+ INSTRUMENTTYPE: LC-ESI-ITFT SMILES: COC(=O)C(CC1=CC=CC=C1)N=C(O)C(N)CC(O)=O INCHIKEY: IAOZJIPTCAWIRG-UHFFFAOYNA-N Ontology: Peptides COLLISIONENERGY: 35 FORMULA: C14H18N2O5 RETENTIONTIME: IONMODE: Positive Comment: registered in MassBank Num Peaks: 9 120.0804 13 180.10201 138 217.0968 14 235.10789 390 245.0921 274 260.09171 132 263.1026 286 277.11859 1000 278.1022 28

Listing S2: Example for the canonical NIST format.

Listing S3: RIKEN PRIME msp format example.

Table S1: Overview of MS/MS handling in different R packages. ‘-’ means not available, for the remaining entries see the text above.

package	read msp	write msp	spectral matching and additional information
baitmet			N vs DB; cosine, Stein & Scott composite similarity product
compMS2Miner	NIST, RIKEN PRIME msp	RIKEN PRIME msp	N vs DB; dot product
enviGCMS		basic NIST
erah	NIST	only result export	N vs DB; cosine
flagme		only result export
metaMS	NIST	NIST; slow	1 vs DB, N vs DB; proprietary
MatchWeiz			N vs DB; X-Rank
MetCirc			N vs N; normalized dot product;
			will switch to MSnbase functions soon
MSeasy		only result export	N vs DB; Queries the NIST mass spectral search tool
MSnbase	**	**	1 vs 1, N vs N; dot product and more, user def.
msPurity			N vs DB; dot product
OrgMassSpecR	basic NIST	basic NIST	1 vs 1; normalized dot product
RAMClustR			RAMClustR can import and utilize spectrum similarities from MS-FINDER;
rTANDEM			N vs DB; dot product; R wrapper for X!Tandem software
SwathXtend	- (PeakView / OpenSWATH)	- (PeakView / OpenSWATH)
TargetSearch	NIST (with error)	NIST	N vs DB; RI-based