MassBank spectrum searches (version 2017-02-06)

File of masses (format: tabular):

Generally variable metadata file

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 (MZ):

Column of pcgroup:

Do you have a column of intensity?:

if 'No' is selected, the value of intensity for each mz is set to 10 (MassBank spectrum search require mz-pcgroup-intensity data - please use massbank peak search if needed)

Column of intensity:

What kind of Ionization Search will be done?:

Score threshold to apply on returned MassBank results:

Default value is 0.5.

Show advanced settings?:

if 'NO' is selected then defaults values are: instruments = all ; max = 10 ; unit = unit ; tolerance = 0.3 ; cutoff = 50 ; server = JP

Wrapping: Franck Giacomoni - PFEM ; INRA ; MetaboHUB (for xml interface and perl wrapper and WS client)

Please cite If you use this tool, please cite MassBank (http://www.massbank.jp)

wsdl_MassBank

Description

Finding information (search spectra method) in the MassBank project via a web service from masses and pcgroups.

Workflow position

/repository/static/images/222d9f655e256f0f/.%2Fstatic%2Fimages%2Fmetabolomics%2Fmassbank-ws.png

Input files

Parameter : num + label	Format
1 : variableMetadata	tabular

File variableMetadata must have at least the 3 following column :

Masses : column with all the masses in the tabular input file
Intensities : column with all the intensities in the tabular input file (Optionnal but if you haven't intensitt values, please use the Massbank peak search tool)
PCgroups : column with all the pcgroups in the tabular input file

Parameters

Number of header lines: Number of lines not containing values
Column of masses: Specify the column number for the mass in the tabular input file
Tolerance of mass (in unit or ppm): Specify a delta (+/-) to the mass to search
Parameters applied on query: cutoff : intensity cutoff (don't add to the query, mz with intensity below defined cutoff).

max: maximum number of records returned by the MASSBANK server foreach pcgroup of masses (by default max is set to 10).

score_threshold: apply a filter on MASSBANK scores (by default threshold is set to 0.5).

mode : Ionization search mode: Positive or Negative ou Both

Instrument: filter applied on spectra depending of the instrument source. (All is the default value) - - GCMS technologies are available in W4M GCMS tools section.

Output files

Two types of files: MASSBANK_WEB.html: for viewing result via HTML.

MASSBANK.tabular: for linking with others modules.

MASSBANK_XLS.txt: an excel-like output to export results under a multi lines format.

MASSBANK_JSON.txt: an json output will be available.

Working example

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

Perform LCMS Annotations

And their "W4M courses 2016":: Using Galaxy4Metabolomics - W4M table format for Galaxy

Annotation Banks - Annotation