pFind Studio: a computational solution for mass spectrometry-based proteomics

pGlyco2 is still improving, any bug or problem, please contact: pglyco[at]ict.ac.cn

Introduction

pGlyco is a software tool designed for the analysis of intact glycopeptides by using mass spectrometry.

The current version of pGlyco is pGlyco v2.1, you can download via this link.

Please cite pGlyco2 via doi:10.1038/s41467-017-00535-2.

New C#/.NET-based GUI has been released, please take a look.

User Guide

1-1: Installation

After downloading pGlyco2, click pGlycoSetup.exe to install pGlyco2, default installation folder is recommended.

1-2: Activation

If it is the first time running pGlyco, an activation window will pop up, as shown below:

pGlyco2 is free software, but we hope you can carefully fill in the registeration form for us while registering.

  • E-mail information is the key information we can contact you.
  • We hope you can fill in the form of "What can pGlyco do for you" as detailedly as you can. Filling in this form with "We use pGlyco to identify intact glycopeptides" makes no sence, because, of course we use pGlyco to identify glycopeptides.

After filling in all the forms, click "Send E-mail", software will send an e-mail to pglyco[at]ict.ac.cn via pglyco[at]126.com, and then we will e-mail you the activation code to your e-mail address.

If "Send E-mail" button does not work (for example your internet is not connected or your firewall prevents pGlyco sending the e-mail), you can alternately send "your_email.pglyco.csv" file in pGlyco2 installation folder to pglyco[at]ict.ac.cn with your own e-mail.

After you get the activation code, click "Have recieved the activation code", import the code file you have recieved.

2: Run pGlyco

After successfully activating pGlyco, run pGlyco again and pGlyco GUI window will pop up, as shown below:

New GUI has for parameter tabs: "MS Data"=>"Identification"=>"Quantification"=>"Check and Run". After setting parameters, click the "Check and Run" Tab, save the parameter, and then click "Start" button to run pGlyco2 core process.

Current version of pGlyco supports RAW and MGF formats, after setting the parameters and clicking "Run pGlyco" button, pGlyco will automatically convert N to J with motif of N-X-S/T/C and parse RAW files by using pParse before pGlyco engine starts. For MGF, pGlyco2 may not support the MGF that extracted by other tools except for pParse, we did not test other MGF formats.

3: Result interpretation

After identification, pGlyco will output parameter file "[task_name].pglyco" and result file "pGlycoDB-GP-FDR-Pro.txt" in the task folder. All results are stored in "pGlycoDB-GP-FDR-Pro.txt", all columns are indexed by headers, including: "GlySpec", "PepSpec", "RT", "PrecursorMH", "Rank", "Peptide", "Mod", "PeptideMH", "Glycan(H,N,A,G,F)", "PlausibleStruct", "GlyID", "GlyFrag", "GlyMass", "GlySite", "TotalScore", "PepScore", "GlyScore", "CoreMatched", "CoreFuc", "MassDeviation", "PPM", "GlyIonRatio", "PepIonRatio", "GlyDecoy", "PepDecoy", "GlycanFDR", "PeptideFDR", "TotalFDR", "Proteins", "ProSite".

  • "GlySpec" and "PepSpec" are the spectrum name ("GlySpec" and "PepSpec" are the same), which contains RAW name, scan number, precursor charge and pParse ID
  • "Glycan(H,N,A,G,F)" refers to the glycan composition identified by pGlyco, H, N, A, G and F are short for Hex, HexNAc, NeuAc, NeuGc and Fuc respectively.
  • "PlausibleStruct" encodes a candidate glycan structure into an canonical code. Decoding of the code:
  • "GlyID" and "GlyFrag" are glycan ID and glycan fragments stored in the glycan database (see pGlyco2 article for details).
  • "GlySite" is the glycosylation site of the peptide.
  • "TotalFDR" is the glycopeptide level FDR which is estimated from "GlycanFDR" and "PeptideFDR" (see pGlyco2 article for details).
  • "Proteins" tells what proteins is the peptide come from. If more than one proteins contain this peptide, they are seperated by "/".
  • "ProSite" stores the glycosylation sites of the proteins with this peptide, they are seperated by "/" as well if there are more than one sites.

4: Simple GPSM annotation with gLabel

After identification, you could run gLabel.bat in pGlyco2 folder, as shown below:

Load "pGlycoDB-GP-FDR-Pro.txt" and MGF file, fill in the "spectrum" with spectrum name and click "show" button, an annotation plot of a GPSM will be shown (plotted by python with matplotlib). Save the plot as .eps format and edit it with Adobe Illustrator, you can get a better-looking plot, like this:

Have fun with pGlyco2!! Do not hesitate to contact us: pglyco[at]ict.ac.cn