Todo MSP Parser

[yguitton]

Todo: add a parser for MSP files generated by MoNa or Riken, Golm
Todo: add additional Tags in metaMS identification outputs

example Riken MSP
NAME: CITRIC ACID-TETRA-TMS; EI-B; MS
EXACTMASS: 480.1851098
FORMULA: C18H40O7Si4
SMILES: CSi(C)OC(=O)CC(CC(=O)OSi(C)C)(OSi(C)C)C(=O)OSi(C)C
ONTOLOGY: Tricarboxylic acids and derivatives
INCHIKEY: VFGAVMGYDWDESE-UHFFFAOYSA-N
RETENTIONTIME: -1
RETENTIONINDEX: 1788.907
QUANTMASS: 75
IONMODE: Positive
COLLISIONENERGY: 70eV
LICENSE: CC BY-SA
Comment:
Num Peaks: 141

[YonghuiDong]

The peak information is misisng In your example MSP file.

In case you are interested, you can refer to the code from @yufree to read MSP files from MoNa or Riken,
https://github.com/yufree/enviGCMS/blob/c458d9458c9348fc62b31caaf1f19bbf111aff15/R/io.R#L112-L158

Yonghui Dong

[valpalgal]

I tried to read in a NIST .MSP file and got the following error:
Error in read.compound(huhn[starts[i]:ends[i]], noNumbers = noNumbers) :
No spectrum found

When I look at the MSP file though, there is a line called "Num Peaks:" that should be detected based on what I'm seeing in the read.msp function for metaMS.

[yguitton]

Hi @valpalgal

There are different "flavours" of NIST .msp spectra files depending on the software/lab used to generate ir. can you share on file with me?

Best