# pGlycoQuant #### Here, we report pGlycoQuant, a generic software tool for quantitative intact glycopeptide analysis, supporting both primary and tandem mass spectrometry quantitation for multiple quantitative strategies. pGlycoQuant advances in glycopeptide evidence matching through applying a deep learning model that reduces missing values for glycopeptide quantification by over 60% compared with Byologic, MSFragger-Glyco and Skyline, as well as an optional function of Match-In-Run (MIR) algorithm for more quantitative coverage of glycopeptides, thus greatly expanding the quantitative function of several powerful search engines, currently including pGlyco 2.0, pGlyco3, Byonic and MSFragger-Glyco. ### Version: pGlycoQuant_v202211 ### Release Date: 2022.11.07 ### We have extend the permission of the core engine to 2023.06.30. ## Computer configuration #### RAM: 16G or higher is recommended #### ROM: for one raw data (1G) 2G or higher is recommended #### OS: Windows10 or higher #### Other: MSFileReader 3.0 Sp1 or higher is needed ## Description #### At present, pFind, pGlyco, Byonic and MSFragger software glycosylation identification results can be used for quantification by pGlycoQuant. ## GUI Operation Usage #### Please read "Manual for pGlycoQuant.pdf" to learn the useage of pGlycoQuant. #### The dataset used for demo also can be found in TEST_DATA folder. ## Other notes ### Notes for running Byonic result #### 1. It is found that the name of mass spectrum data recorded by Byonic software is inconsistent with the original data, when running pGlycoQuant in Byonic mode, it should be guaranteed that the name of the mass spectrum data recorded in the Byonic result file is the same as that of the entered mass spectrum data. #### 2. Byonic glycosylation modification reliable results screening commonly used scores are Score and LogProb, rather than FDR. FDR cannot be modified on the pGlycoQuant interface. To add THRESHOLD_SCORE_BYONIC=XXX and THRESHOLD_PROB_BYONIC=XXX in the config file (default: 200 and 2, indicating score≥200 and absolute value of LogProb ≥2). #### 3. Byonic ini files are required for quantification, in the ./ini/ini_Byonic directory. ### Notes for running MSFragger result #### MSFragger ini files are required for quantification, in the ./ini/ini_MSFragger directory. ## Cite us #### Weiqian Cao, et. al. pGlycoQuant with a deep residual network for precise and minuscule-missing-value quantitative glycoproteomics enabling the functional exploration of site-specific glycosylation. bioRxiv 2021.11.15.468561. #### doi: https://doi.org/10.1101/2021.11.15.468561