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

[valpalgal]

You are right, I changed the formatting of my MSP files to match more or less what I was seeing in your source code. I used text edit commands in terminal to remove the offending lines - some of the annotations for each compound were different than the NIST MSP files and the mass counts were separated by ";" though it looked like you already had code to read that type of separation.

I downloaded the Mass Spectra for Chemical Ecology (Release 6) MSP file. It has the ".mace" file suffix but it is a text file in MSP format. https://leopard.tu-braunschweig.de/receive/dbbs_mods_00078108

[valpalgal]

Oh oops, the metaMS code actually works fine for the MACE database linked above, not for the NIST one though. An example of the NIST MSP file I used is attached.
NIST14_example.txt

I had the reverse issue with the eRah package's database import function - the MACE database won't upload without edits but the NIST database is fine. I didn't try to debug the metaMS code because the NIST file (~270,000 spectra) is so much larger than the MACE file (~500 compounds).