Description

moFF (a Modest Feature Finder) is an OS independent tool designed to extract apex MS1 intensity using a set of identified MS2 peptides. It currently uses a Go library to directly extract data from Thermo Raw spectrum files, eliminating the need for conversions from other formats. Moreover, moFF also allows one to work directly with mzML files.

Usage

Modules:

1. Apex Intensity: this is used for a single pair of files, one identification and one spectrum file.
2. Match between runs (MBR): for multiple identification files, share MS2 identified peptides between runs and predict the retention time.
3. All (match between runs followed by apex intensity): this is used for more than one pair of identification and spectrum files.

If both match between runs and apex intensity are desired, it is best to run them both at once (i.e., run the 'All' module). The MBR module is mainly useful for observing the intermediate steps of the algorithm - its outputs are not able to be used as inputs in moFF or in other tools. If quantification of multiple files without MBR is desired, the apex intensity module may be run with multiple files or a dataset collection in batch mode. In either case, moFF must be given the paired files at the same time - thus the best method is to construct a dataset collection in which the raw and identification files are in the same order.

Inputs:

• Identification file: this can either be a generic tabular file or the standard PSM report from PeptideShaker. If it is a generic tabular file, please select the columns corresponding to the required information.
• MS/MS file: this can either be a Thermo raw file or an mzML file.

A given pair of files must have the exact same display name, not including the extension; e.g. example1.tabular and example1.mzml. If the display names are different, simply change them in the history menu. For multiple files (the MBR or All modules), the identification and spectrum files must be provided as dataset collections. This allows for usage of the output dataset collections in workflows.

Parameters:

All the parameters related to the the time windows (rt_w, rt_p, rt_p_match) are basically the half of the entire time windows where the apex peak is searched or the XIC is retrieved. For correct rt windows, we suggest you set the rt_p value equal to or slighly greater than the dynamic exclusion duration set in your machine. We suggest also to set the rt_p_match always slightly bigger than tha values used for rt_p. Outputs: When used in the single file mode ("Apex intensity" module), the outputs are 2 (or 3) files: a log file, a quantitation file, and (optionally) a peptide summary, with intensities aggregated across peptides. When used in the multiple file mode ("All"), the outputs are a dataset collection of log files (one per identification file), a dataset collection of quantification files, and (optionally) a peptide summary. If used with a generic tabular format, the only columns in the output file are the 7 columns selected while using moFF plus the columns that moFF adds. Other columns are discarded.

More Information

See the moFF Github site at https://github.com/compomics/moFF, and the publication at https://dx.doi.org/10.1038/nmeth.4075