PFLink

PFLink takes a variety of HX/MS file formats and converts them to the HXMS file format.

HXMS files can be processed in PFNet to predict ΔGop for protein residues.

Instructions for how to install and run PFLink locally can be found here: README

The README also details what files from each software you must use to generate an HXMS file.

Basic instructions

Use the Isotopic uptake tab to upload your Isotopic uptake data. Use the Envelope tab in addition to Isotopic uptake data if you have isotopic envelope data (only with HDExaminer at this time).

If you are using the 'Custom' data format or HDX Workbench, please upload it to the Isotopic_uptake data section, regardless of whether you have isotopic envelopes in the file.

Each file upload only accepts one file. The online tool only processes one state/protein at a time within that file.

If you have multiple state/protein(s) in that file, you must select the one you want to process.

You can download example files using the 'Download example data' button below.

The flags-file and custom-format CSV can be found inside the example data download zip.

If the option does not say optional, then it is required.

Example datasets

Isotopic uptake File Uploads (.csv)

Global settings

Flags file (.txt) - optional. A flags file can be used to autofill the global settings. It is not necessary, but it can speed up entering data.

Experimental settings

Protein information

File settings - choose your HDX input file format.

Formats

Protein rename and more - optional. Renames your state/protein in your output HXMS file. As well as forcing a replicate ID or bimodal group

Match data output - optional. Save peak match data in the HXMS file.

Peptide inclusion/exclusion (.csv) - optional. Filters peptides that you want to include/exclude in your output HXMS file.

Filter list type

Submit and output data