HMDB MS search (version 1.7.4)

Would you use a file :

if 'NO' is selected then one or more mass(es) must be entered manually

File of masses (Variable Metadata) :

Generally variable metadata file. Please note : HMDB allows maximum 700 query masses per request

Do you have a header :

if 'YES' is selected then enter your number of header lines

Number of header lines :

number of lines not containing masses

Column of masses :

Mass-to-charge ratio :

Default value is 0.05 for HMDB (mass-to-charge ratio)

Number of maximum entries returned by the query :

Default value is 10 for each queried mz / max is 50

Molecular Species :

Select multiple adducts:

Performing advanced annotation :

Getting more information from HMDB (Inchi, logP, ...) but increase time of tool execution

Verbose level:

Authors Marion Landi, Yann Guitton and Franck Giacomoni

Please cite If you use this tool, please add the following reference: Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0 — The Human Metabolome Database in 2013. Nucleic Acids Res. 2013.

Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, et al., HMDB 4.0 — The Human Metabolome Database for 2018. Nucleic Acids Res. 2018.

Wishart DS et al, HMDB 5.0 - the Human Metabolome Database for 2022, Nucleic Acids Res. 2022.

HMDB MS search

Description

Search informations (like : HMDB id, Name, Adduct, delta mass) on HMDB online bank

with one or more mass(es) in a file or entered manually

Parameter : num + label	Format
1 : File of masses	tabular

File of masses (Generally variable metadata file) must have at least the following column :

Would you use a file: Choose whether the masses are in a file or entered manually

YES (default) : parameters File of masses ; Do you have a header ; Column of masses are visible

NO : parameter Mass to submit is visible

If 'use file'='YES'

File of masses: see "Input files" section above

Tabular file format, Generally variable metadata file
Do you have a header: YES (default) : parameter Number of header lines is visible

NO : all lines are considered to contain masses

If 'have a header'='YES'

Number of header lines: Number of lines not containing masses values, these lines will be ignored

In all header cases :

Column of masses: Specify the column number for the mass in the tsv input file

If 'use file'='NO'

Mass to submit: Specify a list of mass to request

one or more mass(es) entered manually

For a masses list, writes : m1 m2 m3

You must separate yours values with space

dot (.) is for float number

In all cases :

Mass-to-charge ratio: Specify a delta (mass-to-charge ratio) to apply on mass - This value is a float, between 0.0000000000000001 and 10.
Molecular Species: Type of ionization of the molecule : positif, negatif, neutral

Two types of files: HMDB_WEB.HTML: for viewing result via HTML.

HMDB_TABULAR.tabular: for linking with others modules.

HMDB_XLS.txt: an excel-like output permitting manual annotation cleaning.

Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto: Format Data For Postprocessing

Perform LCMS Annotations

And their "W4M courses 2022":: Using Galaxy4Metabolomics - W4M table format for Galaxy

Annotation Banks - Annotation