Data Dictionary

Effective use of pgfinder requires an understanding of the inputs and outputs of the software.

Inputs

pgfinder takes data from mass spectrometry instruments, as well as a “database” of expected masses and some user specified modifications.

FTRS Files

This is a file corresponding to deconvolution data generated by the Byos® software with the extension .ftrs.

MaxQuant Files

MaxQuant Files are output by the MaxQuant software. They are tab separated value (TSV) files with a .txt extension.

Modifications

Any number of modifications can be selected to enrich the search space of the database of masses to which the input data is being compared. Allowed mofifications are:

Modification	Description
Sodium	Search for masses corresponding to sodium adducts
Potassium	Search for masses corresponding to potassium adducts
Anh	Search for anhydromuropeptides
DeAc	Search for deacetylated muropeptides
DeAc_Anh	Search for deacetylated anhydromuropeptides
Nude	Search for muropeptides with an extra GlcNAc-MurNAc disaccharide
Decay	Correct output taking into account in-source decay products
Amidation	Search for Amidated muropeptides
Amidase	Search for peptides resulting from amidase cleavage (GlcNAc-MurNAc loss)
Double_Anh	Search for anhydromuropeptides (2 Anhydro groups)
Multimers	Search for multimers resulting from 3-3 and 4-3 crosslinks
Multimers	Glyco Search for multimers resulting from transglycosylation (no transpeptidation
Multimer Lac	Search for lactyl-peptides multimers
O-Ac	Search for O-acetylated muropeptides

Mass Databases (Lists)

Mass databases are lists of structures and their associated mass. They are in CSV format with a .csv extension. pgfinder has built-in mass lists for Escherichia coli and Clostridium difficle, but can take a different mass list as an input.

Column	Description	Unit
Structure	Structure code	NA
Monoisotopicmass	Monoisotopic mass	atomic mass unit

Outputs

pgfinder outputs CSV (.csv) files. The columns in these files depend on the input file format.

Embedded Metadata

The first column contains the following metadata

Data	Description
`file`	Input data file
`masses_file`	Mass list file
`rt_window`	Retention time window
`modifications`	List of modifications
`ppm`	ppm tolerance
`consolidation_ppm`	ppm tolerance for consolidation
`version`	PGFinder version used in analysis

PGFinder Output

Field	Description
`Metadata`	Metadata about input files.
`ID`	Peak identifier.
`RT (min)`	Retention Time in minutes.
`Charge`	Charge states at which mass was observed. Can be used to work back from monoisotopic mass to the recorded raw mass/charge ratios.
`Obs (Da)`	Observed mass in Dalton (unit)
`Theo (Da)`	Theoretical mass in Dalton (unit)
`Delta ppm`	Change in Parts Per Million (difference between `Obs (Da)` and `Theo (Da)`).
`Inferred structure`	Inferred peptidoglycan structure.
`Intensity`	Intensity of peak in relative units.
`Inferred structure (best match)`	Most likely inferred structure.
`Intensity (best match)`	Intensity of the most likely inferred structure.
`Total Intensity`	Sum of intensities for consolidated structures. Can be used to compare how much material was injected/measured between different runs.
`Structure`	Structure of most likely inferred structure.
`Abundance (%)`	Amount (as a percentage of total intensity) of the inferred structure.
`Consolidated RT (min)`	Consolidated Retention time in minutes of the most likely inferred structure..
`Consolidated Theo (Da)`	Consolidated theoretical mass in Dalton (unit) of the most likely inferred structure.
`Consolidated Delta ppm`	Consolidated change in Parts Per Million of the most likely inferred structure.