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