findMass

SMILES code or compound ID of the molecule. (Numerics
are treated as compound ID).

cpdID_or_smiles

A value that determines whether the files should be handled either as "standard",
if the compoundlist is complete, "tentative", if at least a formula is present or "unknown"
if the only know thing is the m/z

retrieval

<code>"pH", "pNa", "pM", "pNH4", "mH", "mM", "mFA"</code> for different ions 
            ([M+H]+, [M+Na]+, [M]+, [M+NH4]+, [M-H]-, [M]-, [M+FA]-).
Only needed for retrieval="unknown"

mode


Retrieves the exact mass of the uncharged molecule. It works directly from
the SMILES and therefore is used in the MassBank workflow
(<code><a rd-options="" href="/link/mbWorkflow?package=RMassBank&version=2.0.0" data-mini-rdoc="RMassBank::mbWorkflow">mbWorkflow</a></code>) - there, all properties are calculated from the
SMILES code retrieved from the database. (Alternatively, takes also the
compound ID as parameter and looks it up.) Calculation relies on Rcdk.


Workflow to process tandem MS files and build MassBank records.
Functions include automated extraction of tandem MS spectra, formula
assignment to tandem MS fragments, recalibration of tandem MS spectra with
assigned fragments, spectrum cleanup, automated retrieval of compound
information from Internet databases, and export to MassBank records.

RMassBank at Eawag

RMassBank

Workflow to process tandem MS files and build MassBank records

findMass function

SMILES code or compound ID of the molecule. (Numerics
are treated as compound ID).

A value that determines whether the files should be handled either as "standard",
if the compoundlist is complete, "tentative", if at least a formula is present or "unknown"
if the only know thing is the m/z

<code>"pH", "pNa", "pM", "pNH4", "mH", "mM", "mFA"</code> for different ions 
            ([M+H]+, [M+Na]+, [M]+, [M+NH4]+, [M-H]-, [M]-, [M+FA]-).
Only needed for retrieval="unknown"

Retrieves the exact mass of the uncharged molecule. It works directly from
the SMILES and therefore is used in the MassBank workflow
(<code><a href="mbWorkflow" rd-options="">mbWorkflow</a></code>) - there, all properties are calculated from the
SMILES code retrieved from the database. (Alternatively, takes also the
compound ID as parameter and looks it up.) Calculation relies on Rcdk.

findMass: Calculate exact mass

Description

Usage

Arguments

Value

See Also

Examples