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.

We currently provide a simple python-based GUI to run pGlyco2, a C#/.NET-based GUI is on preparing.

User Guide

1-1: Installation

After downloading pGlyco2, unzip the .zip archieve file to any folder. WARNING: Do not unzip the archieve into non-english folder. (注意:不要把pGlyco解压缩到中文目录下。) After that, go to unzipped pGlyco folder, and double click pGlyco.bat to run the software.

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 while registering.

  • E-mail information is the key information we can contact you.
  • We hope you can fill in the form of "What project / purpose you use pGlyco for (detailed information)" 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 "Get activation code (mailto: pglyco[at]ict.ac.cn)", we 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 "Get activation code (mailto: pglyco[at]ict.ac.cn)" 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.csv" file in pGlyco2 folder to pglyco@ict.ac.cn with your own e-mail.

After you get the activation code, click "Have an activation code", and fill in "Enter activation code" with the code you have got.

2: Run pGlyco

After successfully activating pGlyco, click pGlyco.bat again and pGlycoGUI window will pop up, as shown below:

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 "parameters.pglyco" and "pGlycoDB-GP-FDR-Pro.txt" in the output 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 plausible 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