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PLGS specifications


Unique identifier OMICS_32151
Alternative name ProteinLynx Global SERVER
Software type Application/Script
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Maintained Yes


No version available


  • person_outline Team Waters

PLGS citations


Discovery and functional characterisation of a luqin type neuropeptide signalling system in a deuterostome

Sci Rep
PMCID: 5940834
PMID: 29740074
DOI: 10.1038/s41598-018-25606-2
call_split See protocol

[…] MS/MS for a period of 20 sec. MS/MS data were collected over m/z range 50–1950 using m/z and charge state dependent collision energy applied to the trap region. Tandem mass spectra were extracted by ProteinLynx Global Server version 2.5.1 (Waters Corporation, Milford, MA, USA) with charge state deconvolution and deisotoping performed prior to creation of a peak list file for each sample. A peak l […]


The Rab11 binding protein RELCH/KIAA1468 controls intracellular cholesterol distribution

PMCID: 5940305
PMID: 29514919
DOI: 10.1083/jcb.201709123

[…] lyzed using a SYNAPT G2 (Waters Corp.) or QExactive (Thermo Fisher Scientific) mass spectrometer at Osaka University Center for Medical Research and Education. The database search was conducted using ProteinLynx Global Server (v.2.4; Waters Corp.) or MASCOT Server (v.2.3; Matrix Science) software and the International Protein Index database (mouse; v.3.77 or 3.87; EMBL-EBI). […]


Characterizing the Key Metabolic Pathways of the Neonatal Mouse Heart Using a Quantitative Combinatorial Omics Approach

Front Physiol
PMCID: 5904546
PMID: 29695975
DOI: 10.3389/fphys.2018.00365

[…] Relative quantification between samples using precursor ion intensities was performed with Progenesis QI for Proteomics™ Informatics for Proteomics software (Non-linear Dynamics/Waters) and ProteinLynx Global Server (PLGS v3.0) (Laakkonen et al., ). Database searches were carried out against Mus musculus UniProtKB-database (release 2014_11, 33214 entries) with Ion Accounting algorithm us […]


A Carbohydrate Moiety of Secreted Stage Specific Glycoprotein 4 Participates in Host Cell Invasion by Trypanosoma cruzi Extracellular Amastigotes

Front Microbiol
PMCID: 5903068
PMID: 29692765
DOI: 10.3389/fmicb.2018.00693

[…] strain were injected onto an LTQ-Orbitrap Velos (Thermo). Masses from the raw Q-TOF files were corrected using a lock mass of m/z 784.823, and the raw data were converted to the .pkl format using the ProteinLynx Global Server (Waters). Orbitrap raw files were converted into .mgf files using MSConverter. Searches were performed in MASCOT (2.4.1 version) against a Trypanosoma cruzi CL Brener databas […]


An Evolutionarily Conserved Mechanism for Intrinsic and Transferable Polymyxin Resistance

PMCID: 5893884
PMID: 29636432
DOI: 10.1128/mBio.02317-17

[…] , and the resultant peptides were analyzed with a Waters Atlantis C18 column (0.03-mm particle size, 0.075 by 150 mm). Finally, the acquired data were subjected to further analyses through the Waters ProteinLynx Global Server 2.2.5, Mascot (Matrix Sciences), and BLAST against the NCBI nr database. […]


Lysophosphatidic Acid Induces ECM Production via Activation of the Mechanosensitive YAP/TAZ Transcriptional Pathway in Trabecular Meshwork Cells

PMCID: 5896423
PMID: 29677358
DOI: 10.1167/iovs.17-23702

[…] scans for each ion used an isolation window of approximately 3 Da, a maximum of 2 sec/precursor, and dynamic exclusion for 90 seconds within 1.2 Da. DDA data were converted to searchable files using ProteinLynx Global Server 2.5.1 (Waters Corp.) and searched against the human UniProt database (September 2015 release; Cambridge, UK), using Mascot server 2.5 with the following parameters: maximum o […]


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