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

Reference Masses

The reference masses file defines the masses of the building blocks used to determine the mass of target structures (muropeptides). A default file is provided as part of the package but user supplied files can be used instead. The file should be ASCII text CSV (not Excel files) with the following columns.

Column	Description	Units
Code	Encoding of the component	`string`
Mass	Atomic Mass of the component	Daltons
Name	Name of component	`string`

Target Structures

The target structures are species specific and define the muropeptides for which the mass is to be calculated. A number of options are available but users can also supply their own file. The file should be ASCII text CSV (not Excel files) with a single column that defines the structure using the Codes defined in the reference masses file. An example is shown below

Structure
gm |0
gm-gm |0
gm(Anh) |1
gm(-Ac) |1
gm-AEJ |1
gm-AEJA |1
gm-AEJG |1
gm-AEJAG |1
gm-AEJKR |1
gm-AEJ (Anh) |1
gm-AEJA (Anh) |1
gm-AEJA (-Ac) |1

Available species specific target structures currently available.

Bacilus subtilis
Enterococcus faecalis
Enterococcus faecium
Escehrichia coli
Staphylococcus aureus

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.