HR2 formula (version 1.2.0)

Would you use a file :

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

File of masses:

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 Id:

Column of masses (mz):

Delta of mass :

Tolerance should be between 0 and 9.0 Da. Default value is 1.0 mmu

Molecular Species Searched:

Or ionization type of the molecule list. Use neutral only if only if the masses correspond to molecules and not to ions : query doesn't be a [M+H] or [M-H] ion

Please unselect basic atom(s) from following list you want to exclude:

Unselect one or more basic atoms to exclude them from the generated formula proposition

Use all 7 golden rules OR only the first 3 golden rules?:

Use 'only first 3 rules' if you want more empirical formulas

Add some atom(s) from following list if needed:

C, H, N, O and P are available in basic atom section

Do you want to manage custom maximum number atoms?:

To work only with [13]C isotopes for example, use YES - ()Don't forget to select wanted atoms below)

Verbose level:

Authors: HR2 original program and its documentation are Copyright (c) 1992-2005 by Joerg Hau under GNU General Public License ("GPL")

Wrapping: Marion Landi - FLAME ; PFEM ; INRA ; MetaboHUB (for xml interface and Perl wrapper)

Franck Giacomoni - PFEM ; INRA ; MetaboHUB (for xml interface, conda dependancies and Perl wrapper)

Please cite If you use this tool, please cite: Tobias Kind and Oliver Fiehn. (2007). "Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry." BMC Bioinformatics p8:105 http://www.ncbi.nlm.nih.gov/pubmed/17389044

HR2 original program and its documentation are under GNU General Public License ("GPL") : GPL is a"contaminating" license. http://fiehnlab.ucdavis.edu/projects/Seven_Golden_Rules/Software

HR2 formula

Description

Find a formula for the masses

only molecules with carbon (C) will be search

Workflow position

/repository/static/images/849b2c5d70754b11/hr2.png

Input files

Parameter : num + label	Format
1 : variableMetadata	tabular

File variableMetadata must have at least the 2 following columns :

Id : column to identify masses in the csv/tsv input file
Masses : column with all the masses in the csv/tsv input file

Parameters

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

YES (default) : parameters File of masses ; Column of Id ; Number of header ; Column of masses are visible

NO : parameter Mass of the molecule is visible

If 'use file'='YES'

Column of Id: Specify the column number for the id in the csv/tsv input file
Number of header lines: Number of lines not containing values
Column of masses: Specify the column number for the mass in the csv/tsv input file

If 'use file'='NO'

Mass (MZ) 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 :

Delta: Tolerance of the gap in the mass

It should be between 0 and 9.0 mmu
Ionization: Type of ionization of the molecule : positif, negatif, neutral

Use neutral if query doesn't be a [M+H] or [M-H] ion

HR2 knows only the weight of uncharged molecules

so we made a correction to the masses of the value of a proton before the search

if the masses are those from a spectrometry in positive or negatif mode.

neutral : will do a search on the mass unchanged.
Initial charge: Use 0 if the molecule is not basically charged
Exclude some basic atom(s): List of atoms that can be exclude to the molecule : C, N, O, H, P
Golden rules: There are 7 golden rules

Some are too stringent, especially for small molecules

Use 'yes' if you want more empirical formulas
Add some optionnal atom(s): List of atoms that can be searched in addition to the molecule : S, F, Cl, K, Br, Na, 13C

Output files

Two types of files: hr2_VIEW.HTML : for viewing result via HTML.

hr2_TSV.tabular : for linking with others modules.

an excel-like output will be available.

Working example

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

Perform LCMS Annotations

And their "W4M courses 2018":: Using Galaxy4Metabolomics - W4M table format for Galaxy

Les banques d'annotation - Annotation