MFAssignR MFAssignCHO (version 1.1.2+galaxy1)

Data frame of monoisotopic masses:

Data frame containing monoisotopic masses, output from the IsoFiltR function

Data frame of isotopic masses:

Data frame containing isotopic masses, output from the IsoFiltR function

ppm_err:

Error tolerance (ppm) for formula assignment

Ion mode:

The ionization mode.

SN ratio:

Noise multiplier. Recommended value is 6.

Estimated noise:

Estimated noise, either from the KMDNoise or HistNoise function.

Lower limit of molecular mass to be assigned:

Lower limit of molecular mass to be assigned.

Upper limit of molecular mass to be assigned:

Upper limit of molecular mass to be assigned.

Advanceds

Advanced 0

MFAssignR - MFAssignCHO

This tool is the fourth step of the MFAssignR workflow (IsoFiltR -> MFAssignCHO -> RecalList)

MFAssignCHO is a simplified version of MSAssign funcion, which only assigns MF with CHO elements. It is useful for the prelimiary MF assignments prior to the selection of internal recalibration ions in conjunction with RecalList and Recal.

Output:

Unambig - data frame containing unambiguous assignments
Ambig - data frame containing ambiguous assignments
None - data frame containing unassigned masses
MSAssign - ggplot of mass spectrum highlighting assigned/unassigned
Error - ggplot of the Error vs. m/z
MSgroups - ggplot of mass spectrum colored by molecular group
VK - ggplot of van Krevelen plot, colored by molecular group

General Information

Overview

MFAssignR is an R package for the molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements. It contains several functions for the noise assessment, isotope filtering, interal mass recalibration, and MF assignment.

The MFAssignR package was originally developed by Simeon Schum et al. (2020), the source code can be found on GitHub. Please submit eventual Galaxy-related bug reports as issues on the repository.

Workflow

The recommended workflow how to run the MFAssignR package is as follows:

Run KMDNoise() to determine the noise level for the data.
Check effectiveness of S/N threshold using SNplot().
Use IsoFiltR() to identify potential 13C and 34S isotope masses.
Using the S/N threshold, and the two data frames output from IsoFiltR(), run MFAssignCHO() to assign MF with C, H, and O to assess the mass accuracy.
Use RecalList() to generate a list of the potential recalibrant series.
Choose the most suitable recalibrant series using FindRecalSeries().
After choosing recalibrant series, use Recal() to recalibrate the mass lists.
Assign MF to the recalibrated mass list using MFAssign().
Check the output plots from MFAssign() to evaluate the quality of the assignments.

For detailed documentation on the individual steps please see the individual tool wrappers.