MoFF (BioFSharp)

MoFF Module

Namespace: BioFSharp.BioContainers
Assembly: BioFSharp.BioContainers.dll

moFF is an OS independent tool designed to extract apex MS1 intensity using a set of identified MS2 peptides. It currently uses a Thermo library to directly extract data from Thermo Raw spectrum files,
eliminating the need for conversions from other formats. Moreover, moFF also allows to work directly with mzML files.
Input Data: moFF requires two types of input for the quantification procedure
Thermo RAW file or mzML file -and- MS2 identified peptide information.
The MS2 identified peptides can be presented as a tab-delimited file containing mimimal (mandatory) annotation for each peptide.
The tab-delimited file must contain the following information for all the peptides:
'peptide' : peptide-spectrum-match sequence
'prot' : protein ID
'mod_peptide' : peptide-spectrum-match sequence that contains also possible modification (i.e NH2-MLTKFESK-COOH )
'rt': peptide-spectrum-match retention time (i.e the retention time contained in the mgf file; The retention time must be specified in second)
'mz' : mass over charge
'mass' : mass of the peptide
'charge' : charge of the ionized peptide.
 ------ Argentini et al. Nature Methods. 2016 12(13):964–966.

Types

Type	Description
ApexIntensityOptions	Those options run the Apex Intensity module. Around the RT of the input feature, a time window is constructed which results in a local XIC. The peak apex is then located in this local XIC. The log_L_R metric measures the skewness of the peak around the RT of the obtained apex point. The SNR metric provides the ratio of peak height to noise, where the noise value is set as the lowest intensity value in the local XIC. mzML must be specified using --tsv_list \| --raw_list (Ms2PeptidesInputFile & RawFile)
EntireWorkflowOptions	Those options run the Entire Workflow module, which executes both, the Match between runs and Apex Intensity module. The options are identical for both apex and MBR modules. The output for the latter (MBR) is stored in the folder sample_folder/mbr_output, while the former (apex) generates files in the specified output_moff folder.Log files for both algorithms are generated in the respective folders.
InputOption	File input methods for the different run options.
MatchBetweenRunsOptions	Those options run the MBR module, which takes a list of features of interest for a given run, and then matches the corresponding features in other runs. The output will be stored in a subfolder ('mbr_output') inside the specified input folder. The MBR module will consider all the .txt files present in the specified input folder as replicates (to select specific files or different extension, please refer to the example below). The files in sample_folder/mbr_output will be identical to the input files, but they will have an additional field ('matched') that specifies which peptides have match (1) or not (0). The MBR algorithm also produces a log file in the provided input directory.
MoFFParameters	Header type which contains lists of all types for input options.

Functions and values

Function or value	Description
`runApexIntensity bcContext opts` Full Usage: `runApexIntensity bcContext opts` Parameters: bcContext : `BcContext` opts : `MoFFParameters list` Returns: `string`	bcContext : `BcContext` opts : `MoFFParameters list` Returns: `string`
`runApexIntensityAsync bcContext opts` Full Usage: `runApexIntensityAsync bcContext opts` Parameters: bcContext : `BcContext` opts : `MoFFParameters list` Returns: `Async<string>`	Warning 1: In case of 'ApexIntensityOptions.Ms2PeptidesInputFileFolder' and 'ApexIntensityOptions.RawFilesFolder' raw file names MUST be the same of the input file otherwise the script gives you an error ! Warning 2: You can not mix the two input methods ( 'Ms2PeptidesInputFileFolder' / 'RawFilesFolder' and 'Ms2PeptidesInputFile' / 'RawFile' ) otherwise the script gives you an error ! Warning 3: mzML raw file MUST be only specified using 'RawFile' / 'Ms2PeptidesInputFile'. The 'RawFilesFolder' option is not available for mzML files. bcContext : `BcContext` opts : `MoFFParameters list` Returns: `Async<string>`
`runEntireWorkflow bcContext opts` Full Usage: `runEntireWorkflow bcContext opts` Parameters: bcContext : `BcContext` opts : `MoFFParameters list` Returns: `string`	bcContext : `BcContext` opts : `MoFFParameters list` Returns: `string`
`runEntireWorkflowAsync bcContext opts` Full Usage: `runEntireWorkflowAsync bcContext opts` Parameters: bcContext : `BcContext` opts : `MoFFParameters list` Returns: `Async<string>`	The output for MBR (MatchBetweenRuns) is stored in the folder sample_folder/mbr_output, while apex (ApexIntensity) generates files in the specified output_moff folder. Log files for both algorithms are generated in the respective folders. Warning 1: In case of 'ApexIntensityOptions.Ms2PeptidesInputFileFolder' and 'ApexIntensityOptions.RawFilesFolder' raw file names MUST be the same of the input file otherwise the script gives you an error ! Warning 2: You can not mix the two input methods ( 'Ms2PeptidesInputFileFolder' / 'RawFilesFolder' and 'Ms2PeptidesInputFile' / 'RawFile' ) otherwise the script gives you an error ! Warning 3: mzML raw file MUST be only specified using 'RawFile' / 'Ms2PeptidesInputFile'. The 'RawFilesFolder' option is not available for mzML files. You can set all the parameters values in a file and load them using "MoffFile". bcContext : `BcContext` opts : `MoFFParameters list` Returns: `Async<string>`
`runMatchBetweenRuns bcContext opts` Full Usage: `runMatchBetweenRuns bcContext opts` Parameters: bcContext : `BcContext` opts : `MoFFParameters list` Returns: `string`	bcContext : `BcContext` opts : `MoFFParameters list` Returns: `string`
`runMatchBetweenRunsAsync bcContext opts` Full Usage: `runMatchBetweenRunsAsync bcContext opts` Parameters: bcContext : `BcContext` opts : `MoFFParameters list` Returns: `Async<string>`	The output will be stored in a subfolder ('mbr_output') inside the specified input folder. The MBR module will consider all the .txt files present in the specified input folder as replicates. The files in sample_folder/mbr_output will be identical to the input files, but they will have an additional field ('matched') that specifies which peptides have match (1) or not (0). The MBR algorithm also produces a log file in the provided input directory. bcContext : `BcContext` opts : `MoFFParameters list` Returns: `Async<string>`