User Manual 1
Gly-Q™ Glycan
Analysis System
User Manual
Product Code: GQ2100
Version: AF
2 Gly-Q™ Glycan Analysis System
This product is intended for in vitro experimental research use only
Note: The following suggestions and data are based on information we believe to be reliable. They are offered in good faith, but wi thout guarantee, as
conditions and methods of use of our products are beyond our control. We recommend that the pros pective us er determine the suitability of our
materials and suggestions before adopting them on a commercial scale. Suggestions for use of our products or the inclusion of descriptive materia l
from patents and the citation of specific patents in this publication should not be understood as recommending the use of our products in violation of
any patent or as permiss ion to license to use any patents of ProZyme, Inc.
User Manual 3
CONTENTS
Section 1: Safety Information ..............................................................................................................................................4
Section 2: Introduction ........................................................................................................................................................5
2.1 The Gly-Q System ................................................................................................................................................. 5
2.2 Description of System Components .................................................................................................................. 5
2.2.1 Gly-Q Instrument......................................................................................................................................... 6
2.2.2 Gel Recharging Air Pump ........................................................................................................................... 7
2.2.3 Cartridge Priming Station........................................................................................................................... 7
2.2.4 Replaceable Capillary Gel Cartridge......................................................................................................... 8
2.2.5 Sample Preparation and Analysis Kits ..................................................................................................... 9
2.2.6 Glycan Standards.......................................................................................................................................10
2.2.7 Gly-Q Manager Software .........................................................................................................................11
Section 3: Ins tallation.........................................................................................................................................................13
3.1 Unpacking............................................................................................................................................................ 13
3.2 System Location ................................................................................................................................................. 13
3.4 Computer Requirements ................................................................................................................................... 13
3.5 System Set-up ..................................................................................................................................................... 14
3.6 Software Installation ......................................................................................................................................... 15
3.7 Cartridge Prepa ration ....................................................................................................................................... 16
3.7.1 Compon ents ...............................................................................................................................................16
3.7.2 Unpacking and Preparing the Cartri dge ................................................................................................16
3.7.3 Priming the Cartridge ...............................................................................................................................17
3.7.4 Inserting the Cartridge into the Instrument .........................................................................................18
3.8 Ending a Run ....................................................................................................................................................... 18
3.9 Vacuum Manifold Setup ................................................................................................................................... 19
Se cti on 4: Gly-Q Manager Software ..................................................................................................................................20
4.1 Starting Gly-Q Manager.................................................................................................................................... 20
4.2 Controlling and Monitoring Gly-Q Instrument.............................................................................................. 20
4.3 Creating a Sequen ce .......................................................................................................................................... 21
4.3.1 Import & Export.........................................................................................................................................22
4.3.2 Sequenc e Preview .....................................................................................................................................22
4.3.3 Autosampler Layout..................................................................................................................................22
4.4 Running a Sequence .......................................................................................................................................... 23
4.4.1 Starting and Stopping a Sequence .........................................................................................................23
4.4.2 Moni toring Sequence Progress...............................................................................................................24
4.5 Data Review, Export, Reporting and Management ..................................................................................... 25
4.6 Creating a Processing Method ......................................................................................................................... 31
4.7 Creating an Instrument Method ...................................................................................................................... 34
4.8 Ending a Run ....................................................................................................................................................... 36
4.9 File Settings ......................................................................................................................................................... 37
Section 5: Care and Maintenance ......................................................................................................................................39
Section 6: Sys tem Specifica tions........................................................................................................................................40
Section 7: Warranty Statement .........................................................................................................................................41
Section 8: Ins tructions for Depot Repair Returns ..............................................................................................................42
Section 9: FAQs ..................................................................................................................................................................44
Section 10: Legal Notices ...................................................................................................................................................48
10.1 Trademarks & Tradenames............................................................................................................................ 48
10.2 ProZyme Virtual Patent Marking .................................................................................................................. 48
Section 11: Resources and References ..............................................................................................................................49
Section 12: Technical Assistance........................................................................................................................................50
4 Gly-Q™ Glycan Analysis System
SECTION 1: SAFETY INFORMATION
The Gly-Q system is intended to be installed and operated by the end user. To operate the system safely
please review the following information.
Warning:
Both the instrument and the gel recharging air pump must be
connected to an appropriate power source. (See Section 6:
System Specifications)
Warning:
Do not operate the system if any of the power cords are
damaged.
Warning:
The Gly-Q system is based on capillary gel electrophoresis
separation driven by high voltage. Do not remove covers. Do
not perform any maintenance of the electrical components.
Caution:
The instrument autosampler rotates and moves during
operation. Keep the instrument door closed while running to
avoid potential pinching hazard. Do not put your hands into
the autosampler chamber unless the instrument is put into
either the “Load Reagents” position or the “Load Samples”
position and the autosampler has stopped moving.
Caution:
Follow local biohazard material handling regulations when
working with human or animal samples.
Suggestion: Wear appropriate gloves when handling samples
and reagents used with the system.
Caution:
Always turn off the power to the gel recharging air pump when
emptying the condensation trap.
User Manual 5
SECTION 2: INTRODUCTION
2.1 The Gly-Q System
The Gly-Q System is designed as a complete system for rapid analysis of oligosaccharides such as glycans.
The system is comprised of capillary gel electrophoresis core integrated with a high sensitivity fluorescence
detector and 96-well autosampler, replaceable capillary gel cartridge, gel recharging pump, Gly-Q Manager
software and InstantQ assay kits and standards.
2.2 Description of System Components
The Gly-Q System components are listed below and described in more details in the sections that follow:
Gly-Q Instrument – Product Code GQ2000
Gel Recharging Air Pump – Product Code GQ2000-A
Replaceable Capillary Gel Cartridge
Assay Kit
Standards and Controls
Gly-Q Manager Software
Cartridge Priming Station
Gly-X Manifold Spacer
• 8
6 Gly-Q™ Glycan Analysis System
2.2.1 Gly-Q Instrument
The Gly-Q Instrument is a compact unit comprised of a capillary gel electrophoresis core integrated with a
high sensitivity fluorescence detector and 96-well autosampler. When used as part of a complete system,
the instrument facilitates rapid separation, identification and relative quantitation of labeled
oligosaccharides. See Sec tion 6: System Specifications for instrument specifications.
Feature
Description
Instrument status LED
LED light serves as an indicator of the instrument status. The
light blinks when high voltage is applied to the capillary.
96-well plate
autosampler
The autosampler holds a 96-well microplate, system reagent
vials and reagent trays. The autosampler moves and rotates
during operation. The autosampler interior is protected by a
hinged plastic door.
Power button
The power button turns the instrument On and Off.
Air pressure gauge
Air pressure gauge displays inlet air pressure.
Air inlet port
1/8 inch tube connector used for connecting instrument to
gel recharging air pump.
USB port
Computer port.
Power inlet
Power supply port.
Cartridge
compartment door
Instrument status
LED
96-well plate
autosampler
Power button
Air pressure gauge
Air inlet port
USB port
Power inlet
Instrument label
Front
Back
User Manual 7
2.2.2 Gel Recharging Air Pump
The gel recharging air pump connects to the instrument and provides air pressure for automated recharging
of the capillary with gel between sample injections. See S ec tion 6: S y stem Specifications for pump
specifications.
Feature
Description
Air tubing (not
shown)
1/8 inch tubing connects the pump to the instrument.
Power switch
Power switch turns the pump On and Off.
Condensation trap
Condensation trap collects condensate from air pump. This should
be emptied weekly as routine maintenance.
Air outlet port
1/8 inch tube connector used for connecting gel recharging air
pump to Instrument.
Power inlet (not
shown on the back
of the unit)
Power supply port.
2.2.3 Cartridge Priming Station
The cartridge priming station is designed to prepare the cartridge for first-time use before installing it into
Gly-Q Instrument. The priming station can also be used to help troubleshoot cartridge clogging.
Condensation trap
Power switch
Air outlet port
8 Gly-Q™ Glycan Analysis System
2.2.4 Replaceable Capillary Gel Cartridge
The replaceable capillary gel cartridge contains a 147-mm capillary mounted into the cartridge body with a
gel matrix top reservoir and built-in electrode pins. The capillary is automatically refilled with gel matrix
between sample runs.
Feature
Description
Capillary
Glass capillary.
Note: fragile glass tip extends beyond metal cartridge tip
Anode pin
A pin that connects to a positively charged electrode
Cathode pin
A pin that connects to a negatively charged electrode
Label
Cartridge label with lot number and expiration date
Gel reservoir
Top reservoir containing separation gel
Guiding groove
Molded groove ensures correct cartridge positioning within the instrument
Cartridge tip
Metal tip of the cartridge
Cartridge Tip
Anode Pin
Cathode Pin
Capillary
Gel Reservoir
Label
Guiding Grove
Glass Capillary Tip
User Manual 9
2.2.5 Sample Preparation and Analysis Kits
Gly-X N-Glycan Rapid Release and Labeling Kits
ProZyme Gly-X sample preparation kits utilize a novel in-solution enzymatic deglycosylation followed by
labeling of released N-glycans with proprietary ProZyme Instant dyes. Gly-X with InstantPC (GX96-IPC) is
designed for UHPLC and LC-MS applications. Gly-X with InstantQ (GX96-IPC) is specifically designed for CE
separation on the Gly-Q System. Labeling (1 minute) with InstantQ dye is followed by a simple 96-well
vacuum plate-based clean up step. The samples are then ready for analysis on the Gly-Q Instrument. With
the deglycosylation and labeling all carried out in solution, the method is simple, rapid and suitable for
automation.
Feature
Description
Gly-X
Deglycosylation
Module for
InstantQ Dye
GX 96-300
Reagents and consumables for rapid in-solution protein deglycosylation:
• Gly-X Deglycosylation Plate
• Gly-X N-Glycanase
• Gly-X Digestion Buffer
• Gly-X Denaturant
• Gly-X Blocker (optional)
Gly-X InstantQ
Labeling Module
GX 96-301
Dye and solvents for instant labeling of released glycans:
• InstantQ Dye
• InstantQ Dye Solvent
• InstantQ Activation Reagent
Gly-X InstantQ
Cleanup Module
GX 96-302
Clean up plate, eluent and plastic consumables for sample clean-up before analysis:
• InstantQ Cleanup Plate A, 96 wells
• Gly-X Collection Plate, 96 wells
• Waste Tray for vacuum manifold
• Gly-X Used-Well Sealing Caps, Black (for cleanup plate)
Gly-Q Cartridge
Module
GQ 103
Gly-Q Cartridge, Separation Buffer, mineral oil and Reagent Tray:
• Gly-Q Cartridge
• Gly-Q Separation Buffer
• Gly-Q Mineral Oil
• Gly-Q Reagent Tray
Gly-Q Alignment
Standards Module
GK SQ-505
• Gly-Q Migration Standards (GKSQ-500)
• Gly-Q GU Ladder (GKSQ-503)
Labeling module
Clean-up module
Cartridge module
Deglycosylation module
10 Gly-Q™ Glycan Analysis System
Note: See the Gly-X Rapid N-Glycan Release and Labeling with InstantQ kit (GX96-IQ) user manual for
more detailed product and protocol information.
Note: GX100 Gly-X Manifold Spacer is required for the Gly-X Rapid Release and Labeling with InstantQ
Dye Kit.
2.2.6 Glycan Standards
2.2.6.1 Gly-Q Alignment Standards
Gly-Q glucose unit (GU) Ladder is generally the first run at the beginning of each sample sequence and
produces >15 peaks in the electropherogram (see below). The Migration Standards (MS) co-injected with
subsequent unknown samples will be aligned to the Maltodextrin (GU) ladder for glycan naming and
alignment purposes.
Gly-Q Migration Standards (MS) are co-injected along with each unknown sample. A lower migration
standard (LMS) and upper migration standard (UMS) corresponding to 3 and 15 glucose units respectively is
used to align with the above described Maltodextrin (GU) ladder.
2.2.6.2 InstantQ Glycan Standards
Standards are highly purified and well characterized individual oligosaccharides or mixed libraries of
oligosaccharides. They are used for Gly-Q method calibration and validation. For the list of available InstantQ
Standards and Controls, please refer to the following website links:
• InstantQ Labeled Oligosaccharides
prozyme.com/collections/instantq-standards
LMS
UMS
User Manual 11
2.2.7 Gly-Q Manager Software
The Gly-Q Manager software controls Gly-Q instrument, collects and processes data, and reports results. The
software features are organized into tabs and ribbon groups for easy intuitive navigation:
Feature
Description
File tab
File tab enables and informs the user:
• Serial Number of Instrument and Cartridge
• Gly-Q Manager software version
• Air Flow Check
• Gel Flow Check
Sequence Tab
Sequence tab enables:
• Access to the autosampler
• Programming a sequence
• Starting and Stopping a sequence
• Monitoring sequence operations in real-time
File
Sequence
Data
Processing Method
Instrument Method
Instrument Status Bar
12 Gly-Q™ Glycan Analysis System
Feature
Description
Data tab
Data tab enables:
• Data review
• Integration adjustment
• Data reprocessing
• Data export/reporting
Processing
Method Tab
Processing method tab enables:
• Processing method design
Instrument
Method tab
Instrument method tab enables:
• Instrument method design
• Saving an Instrument Method
Instrument
Status Bar
Instrument Status Bar informs the user:
• Instrument connectivity
• Progress of run
• Estimated finish time of run
Note: See Section 4 for more detailed description of Gly-Q Manager functionality.
User Manual 13
SECTION 3: INSTALLATION
3.1 Unpacking
Inspect shipping boxes. If you notice apparent damage, contact ProZyme Technical Support, (800)457 -9444
(US & Canada); +1 510-683-6900; info@prozyme.com
Unpack the system components and place them on the laboratory bench.
Note: The Gly-Q Instrument contains sensitive optics that can be influenced by condensation. If the
instrument was shipped in cold weather, do not remove the instrument from the shipping box
immediately, allow it to warm up to room temperature.
3.2 System Location
A suitable environment is important to ensure the best performance of the Gly-Q System. The recommend ed
placement conditions are listed below:
• Flat and stable laboratory bench with no devices generating vibrations
• Clear space above the instrument to allow for capillary gel cartridge insertion
• Clear space behind the instrument to allow for air circulation, electrical and air tubing connections
• The ambient temperature should be stable and within a range of 20-30 °C
• The optimal operating humidity should be within 40-95% RH range, non-condensing
• The optimum altitude for Gly-Q System operation is 20-2000 m
3.3 Power Requirements
The input voltage of Gly-Q Instrument is 24V DC and the maximum current is 1.25A. A suitable power
supply with a power cord is included in the package (100-240V AC, 47-63Hz). See Section 6: System
Specifications.
The input voltage of Gly-Q System gel recharging air pump is 12V DC and the maximum current is 6.67A. A
suitable power supply with a power cord is included in the package (100-240V AC, 47-63Hz). See Section 6:
System Specifications.
3.4 Computer Requirements
• Operating System Windows 7, 8.1 or 10; 64-bit version
• Processor 1 GHz or faster CPU
• Memory Minimum 8 GB RAM
• Disk Drive 1 TB Hard Disk Drive or 500 GB Solid-State Drive preferred
• Disk Space Minimum 100 GB free space on drive (Solid-State Drive recommended)
• Monitor Minimum resolution 1920 x 1080 (Full HD)
• Graphics Card Supports Full HD (1920 x 1080 resolution)
• Port USB 2.0 or greater
14 Gly-Q™ Glycan Analysis System
3.5 System Set-up
Plug the air pump power supply, Gly-Q Instrument power supply, computer and monitor into approved
and properly grounded power outlets. A surge protector is suggested to minimize power fluctuations.
Plug each power supply low voltage line into the power inlet of the appropriate unit (Gly-Q Instrument
power inlet and air pump power inlet). The two connectors are different to prevent using the wrong
power supply.
Connect computer and Gly-Q Instrument with USB cable.
Connect air pump outlet and Gly-Q Instrument air inlet port with provided 1/8-inch tubing. The airline
from the air pump to the instrument is bisected by an air filter.
Note: After turning on the air pump it should run intermittently for less than 1 minute. If the air pump is
running more consistently this is a sign of air pressure compromise that may affect performance. The
user should check the air filter and tubing for possible leaks. Spare tubing and replacement air filter are
shipped with the instrument. Contact ProZyme if you need assistance.
User Manual 15
3.6 Software Installation
Log into PC as Administrator.
Download the latest version of Gly-Q Manager from the ProZyme website:
http://prozyme.com/products/gly-q-manager-software-gqsw2000
Note: Please contact ProZyme for password information
Double click on the .exe file, click on Gly-Q Manager Setup.
Go through software installation steps.
Note: If you have an older version of Gly-Q Manager software installed on your computer, you will be asked
to uninstall it prior to installing a newer version. Installing new version of Gly -Q Manager won’t delete
data. All user data will be preserved during installation.
16 Gly-Q™ Glycan Analysis System
3.7 Cartridge Preparation
3.7.1 Components
3.7.2 Unpacking and Preparing the Cartridge
Open gel-cartridge clam-shell container and remove the cartridge
Peel off the tape from side and top of cartridge (retain top tape for storage of cartridge between uses)
.
Capillary gel cartridge clam-shell container (keep this for
storage between uses)
Tape on cap (red, keep this for storage between uses)
Pin used to puncture the cartridge cap (white) prior to
initial use
Gel reservoir. Store the tip of the cartridge in the gel
reservoir inside the clam-shell container
User Manual 17
Carefully remove and pin from package. Insert pin into the hole of the cartridge cap and push it down
to the end. Slight resistance should be encountered when performing this step.
3.7.3 Priming the Cartridge
Turn off the Air Pump and use the illustration to reconnect the air tubing.
Put a buffer tray at the bottom of purge station
Slide the cartridge into the Cartridge Hanger and secure
by turning the Locking Knob as illustrated.
Push the knob on top of the regulator down
Turn Air Pump ON
Pull Regulator Knob UP and turn CLOCKWISE to open
airflow until pressure reaches ~ 0.5 mPa.
Droplets of gel should be observed flowing at cartridge
tip in ~ 30-120 sec
Turn the Regulator Knob COUNTERCLOCKWISE until the
airflow is OFF
Once the pressure returns to 0, push the Regulator
Knob DOWN
Slowly release the cartridge and remove from priming
station
Regulator knob
18 Gly-Q™ Glycan Analysis System
3.7.4 Inserting the Cartridge into the Instrument
Gently wipe the cartridge tip with Kimwipe or similar tissue.
Note: the glass capillary extends beyond the end of the metal tip, and is fragile, handle with care, do not
tap tip on bench or hard surfaces.
After gently depressing cartridge door atop Gly-Q Instrument insert cartridge and close door. Push the
cartridge to the Bottom
Note: Cartridges can only be inserted in one orientation as shown in figure above.
Close Cartridge Door
Note: Dispose of spent cartridges by using a needle clipper, available with most sharps hazard systems to
remove cartridge tip. The remaining cartridge is safely disposed of as trash. The clamshell package
can be added to most plastics recycling streams.
3.8 Ending a Run
1. After samples have been processed, the system will return the Cartridge to the Park position (see
section 4.3, autosampler layout).
2. Use the “Load Sample” and “Load Reagents” buttons to remove sample plate and reagent tray.
3. Store the cartridge.
a. Remove the cartridge from the instrument and place tape over the cartridge cap (to
cover the pin hole). Return it to the original clamshell packaging. The cartridge tip must
be in contact with the gel block inside the package. Place inside the foil pouch and store
vertically at room temperature.
b. To store on the instrument: Press the Park button before shutting down the system. The
cartridge can remain on the system for up to 3 days. Ensure that the Park position in the
buffer tray (Section 4.4.3) is filled with water to prevent the capillary tip from drying.
User Manual 19
3.9 Vacuum Manifold Setup
ProZyme recommends the use of Millipore MultiScreen™ Vacuum Manifold (96 -well) and Millipore High
Output Pump (WP6211560 for 115 V/60 Hz or WP6222050 for 220 V/50 H z)
Assemble vacuum manifold.
Connect vacuum manifold and pump inlet with tubing via liquid trap reservoir.
Plug pump into an approved and properly grounded power outlet.
Note: For more detailed product information please refer to Millipore website:
http://www.emdmillipore.com/US/en/product/MultiScreen%E2%84%A2-Vacuum-Manifold-96-well,MM_NF-MAVM0960R#overview
https://www.emdmillipore.com/US/en/product/High-Output-Pump,-115-V60-Hz,MM_NF-WP6211560
20 Gly-Q™ Glycan Analysis System
SECTION 4: GLY-Q MANAGER SOFTWARE
4.1 Starting Gly-Q Manager
To start the Gly-Q Manager double-click the Gly-Q Manager icon on the desktop or select Start -> Gly-Q
Manager.
4.2 Controlling and Monitoring Gly-Q Instrument
To control and monitor the Gly-Q Instrument with Gly-Q Manager, the instrument must be turned on and
connected to a computer via USB cable.
The samples are always analyzed as part of a sequence using a predefined set of instrument commands
stored in an Instrument Method and a predefined set of processing commands stored in a Processing
Method.
When an analysis is running, you can monitor instrument operation via a status bar located at the bottom of
the Gly-Q Manager screen and observe real time detector signal and sequence progress on the autosampler
layout and sequence progress table.
Direct instrument controls are accessible via the Sequence tab:
Park Cartridge moves cartridge into Park position for short term storage on the instrument (up to 3
days).
Load Samples control rotates the autosampler for access to the sample loading stage.
Load Reagents control rotates the autosampler for access to load reagents including GU Ladder and
Migration Standards.
User Manual 21
4.3 Creating a Sequence
A sequence defines how a group of samples is analyzed. Sequence can be created on the Sequence tab by
defining the following fields:
Project & Run
Name your project by selecting “New Project” from the pull down, or select from the list of existing
projects.
Name your run
Methods
Select Instrument Method
Select Processing Method
Note: Default Instrument Methods are recommended. See sections 4.6 and 4.7 on how to create
Instrument Methods and Processing Methods.
Sample Set
Define the position of the first sample
Define the direction the samples will be injected (↔ or ↕)
Define the number of samples to be analyzed
Define the number of injections (number of replicates for each sample)
Note: Changes are saved automatically, and users are advised to double check these settings before
starting a run. If needed, type sample names and comments into the sequence preview table or
import sample set list from Excel (see import CSV below)
22 Gly-Q™ Glycan Analysis System
4.3.1 Import & Export
Export feature allows for exporting a sequence in CSV (.xls) format
Import feature allows for importing a sequence in CSV (.xls) format
4.3.2 Sequence Preview
After a sequence is created, a table with a list of samples queued for analysis will be displayed on the main
screen.
4.3.3 Autosampler Layout
The autosampler layout will show color coded positions for samples, reagents and standards.
Reagent Tray for:
(P) Park; 4 ml DI water + mineral oil
to cover, optional
(W) Wash/Waste; 4 ml DI water
(C) Clean; 4 ml DI water
(S) Separation Buffer; 4 ml, included
with Gly-Q Cartridge Module
P
W SC
User Manual 23
Sequence Status Bar
An instrument status bar at the bottom of the screen will display instrument status:
Sample name
Instrument method step
Well position
Sequence progress and estimated time of completion
Cartridge injection counter
System Pressure
Instrument status
4.4 Running a Sequence
4.4.1 Starting and Stopping a Sequence
After a sequence is created it can be run by clicking on Start button.
Note: If the system cannot read the information on the cartridge RFID tag the dialog shown below opens
allowing the information to be entered manually. The information is on the cartridge and on the pouch
used to store the cartridges between use. To activate the ‘Run’ button enter the cartridge serial
number and use the ‘date picker’ control shown circled in blue to enter the expiration date.
Note: Make certain there is a cartridge installed in the instrument. If there is no cartridge in
the instrument, then the system assumes the RFID tag is damaged and presents this dialog.
If a warning or error message regarding injection limits appears when starting a run refer to the FAQ section.
A sequence can be stopped by clicking on Stop button:
24 Gly-Q™ Glycan Analysis System
4.4.2 Monitoring Sequence Progress
Sequence progress will be displayed on 4 elements of the screen:
Sequence progress bar at the bottom of the screen will show time remaining for sequence completion.
The electropherogram chart will show real time detector signal.
The autosampler layout will show completed samples (green), failed samples (red), currently running
sample (blue) and queued samples (grey).
The sequence progress table will be updated with currently running sample highlighted in darker gray.
User Manual 25
4.5 Data Rev iew, Export, Reporting and Management
After data for all samples in a sequence have been acquired and processed, it is useful to review
electropherograms and peak tables before reporting the results. Peak integration may need to be adjusted
before results are reported. This work is done on the Data tab shown below.
Select the Data tab:
Data Tab
The Data tab includes the following 4 areas:
Data View Ribbon – this includes tools to adjust and to export data
Data Files tree – the data you wish to work on is selected here
Electropherogram – this is the data display which can include 1 or more samples
Samples table – this is a list of the data that has been selected using the Data Files tree. This table is
used to select the samples that will be displayed on the Electropherogram and to review the peak
table for the selected samples.
26 Gly-Q™ Glycan Analysis System
On the Data Files tree, select the sample set:
Data Files
On the Data View ribbon, select processed or raw data view and decide to show or hide annotations and
instrument current signal:
Data View
Note: Always start with processed data view with or without annotations. Raw data view and current
are designed to aid in troubleshooting.
On the Sample table, select the sample(s) you want to view:
Samples
User Manual 27
Open the peak table for any or all of the samples selected by clicking on sign before the sample
name:
Samples
Review peak detection and integration by highlighting peak line in the peak table and reviewing peak
start and end markers on electropherogram view. If needed, zoom in with a left mouse click/hold;
zoom out with a right mouse click and selecting un-zoom.
Electropherogram
Note: In rare circumstances, the Lower Migration Standards (LMS) or Upper Migration Standards
(UMS) may require manual adjustment. Please see the FAQs in Section 9 for further information.
To make sure all peaks of interest are detected, adjust minimum peak area:
Minimum Percent Area Adjustment
Note: This slider is only active when a single sample is selected in the Samples table. You cannot adjust
the minimum percent area on more than one sample at a time.
28 Gly-Q™ Glycan Analysis System
Reprocessing data. In some cases, one or more samples within a data set need to be reprocessed. To
do this select the sample(s) to be reprocessed on the Samples table (NOT the Data Files tree). Multiple
samples can be selected in the Samples table and all selected samples will be displayed in an overlay
electropherogram plot as shown below. This facilitates sample comparison and allows reprocessing to
be performed simultaneously on more than one sample. Use “Shift+Click” and/or “Control+Click” to
select multiple samples as shown below.
Selecting Multiple Samples
Example using “Control+Click” to select non-adjacent samples
Note: When more than one sample is displayed in an overlay electropherogram plot hovering the
mouse over one of the plots will highlight the plot itself and the corresponding row in the
Samples table. Conversely, hovering the mouse over a row in the Samples table will highlight
sample in the table and the corresponding plot in the electropherogram.
In some cases, data from different data sets must be reprocessed in an identical manner. Select data
from multiple data sets in the Data Files tree and it will all be displayed in the Samples table. To reprocess
them all together you must combine them into a Virtual Data Set because reprocessing is restricted to
data within a single data set. To create a Virtual Data set first highlight the desired samples in the Sample
table and then right click on any of the selected samples and select “Create Virtual Data Set” in the pop -
up menu.
User Manual 29
A dialog opens to name the Virtual Data set.
Select the desired project, enter the desired names, and if desired select a calibration ladder. Click on
the “Create” button and the new Virtual Data Set will appear in the Data Files tree. Click on this data set
and only the samples included in the Virtual Data Set will be in the Samples table and only the first
sample will be selected and displayed. Before proceeding use “Shift+Click” or “Control+Click” to select
the other samples in the Virtual Data Set.
To reprocess the data selected in the Samples table, select the desired Processing Method and click Process:
Data Processing
The new processing method will be displayed in the Processing Method column in the Samples table
which is immediately to the right of the Sample Name.
After review, data can be exported in QDF, PDF, CDF or CSV formats:
30 Gly-Q™ Glycan Analysis System
Export & Reporting
• Selecting QDF export will create a file readable by Gly-Q Manager. This is particularly useful for sharing
data with fellow researchers.
• Selecting PDF export will create an electronic report that can be printed. The report will include
electropherograms and peak data tables for selected samples. The header of the report can be
customized in the File tab.
• Selecting CDF export will create a set of files in the industry standard AIA format that can be viewed
by other analytical data packages such as Chromeleon and Empower.
• Selecting CSV export will create two files for selected samples: a file with peak table data and a file
with XY data.
Data Management: Archive and Delete
Over time the number of projects increases hence it becomes more difficult to find the data you are
looking for. To simplify searching for data in the database you can archive and delete projects.
The data files tree is shown in 3 pictures below. On the left the selected project is under ‘Projects’ which is
the active database. In the center the selected project is under ‘Archive’ which is used to hold valuable
projects that will not be accessed frequently outside of the active database. On the right the selected
project is under ‘Trash’ which is used to place projects which are no longer needed.
The 3 buttons used for data management are shown in the picture above.
• The ‘Archive’ button is used to move projects from the active database into the archive.
• The ‘Restore’ button is used to move projects from either the archive or the trash into the active
database.
• When the selected project(s) is in the active database or the archive the ‘Delete’ button moves
them to the trash.
• When the selected project(s) is in the trash the ‘Delete’ button will remove the project entirely.
Note: The functions of these buttons can also be accessed by using right-clicking on the selected
project(s).
User Manual 31
4.6 Creating a Processing Method
Processing method defines peak alignment, peak integration and peak calling. Gly-Q Manager installs
equipped with several examples of processing methods.
• Enbrel_Method: contains GU values for InstantQ-labeled N-glycans from Enbrel (Fc fusion protein)
produced in CHO. Mainly biantennary glycans, some with α(2,3)-linked sialic acid, with some
Man5.
• Global_Method: GU values for a broad range of N-glycans, combining the data from all processing
methods listed.
• hIgG_Method: N-glycans from human IgG, biantennary, some with α(2,6)-linked sialic acid, some
with bisecting GlcNAc. For glycoproteins produced in CHO use the Enbrel or Rituxan processing
methods. Glycoproteins made in CHO generally lack bisecting GlcNAc N-glycans, sialic acid is
α(2,3)-linked in CHO vs. α(2,6)-linked in human IgG, and human IgG does not contain a significant
amount of high mannose type glycans.
• Rituxan_Method: N-glycans from Rituxan, monoclonal IgG made CHO. Biantennary, some high
mannose.
• RNAseB_Method: high mannose type N-glycans, Man5 through Man9.
While these methods can be used as a starting point, each laboratory is expected to develop and validate a
processing method that meets the needs of a specific application.
To create or modify a processing method, select the Processing Method tab and pick one of the existing
processing methods from the drop-down menu:
Processing Method Tab
In the Representative Sample tab, select a sample that most closely matches the samples you plan to
process.
32 Gly-Q™ Glycan Analysis System
Open the peak table by clicking on sign and review peak integration:
Samples Table
Review peak detection and integration by highlighting peak line in the peak table and reviewing peak
start and end markers on Electropherogram view. If needed, zoom in by clicking and dragging a rectangle
around the area of interest; zoom out with a right mouse click and select un-zoom.
Electropherogram
User Manual 33
In the Integration Parameters Tab there are four parameters available.
• Select the Baseline Valley-to-Valley Modulation level. A setting of 100% is recommended, 0% is a
flat baseline, and 50% is half way between these settings.
• Select whether Detect Shoulders should be used. Checked will detect peak shoulders as separate
peaks and is recommended, un-checked will identify peak with shoulders as a single peak.
• Adjust the Minimum Percent Area using the slider or by entering a number directly until all peaks
of interest on the representative sample electropherogram are displayed.
• Select the Processed Data Range by entering a left window value and a right window value. Settings
of 4 and 14 are recommended. If the window is set outside of the LMS and UMS, these Migration
Standards will be omitted from the percent area calculations.
In the Component Table tab, check the Glycan Naming checkbox, define Peak Names, GU Units and
Left and Right Windows. The empty row at the bottom of the table can be used to add Glycans to
the table.
Note: The Left Window and Right Window value controls will simultaneously change all values in the
table that are currently set to the value displayed in the controls. Values in the table that are not the
same as the values in the controls will not be changed.
34 Gly-Q™ Glycan Analysis System
In the Alignment tab, define Lower and Upper Migration Standards, select Predictive UMS Search
(checked is recommended), and check Dextran Ladder Rule:
Save the Processing method by clicking on Save or Save As.
Note: After a processing method has been applied to a data set we recommend usi ng ‘Save As’ if you wish
to make changes to the method.”
4.7 Creating an Instrument Method
Instrument method defines a set of instrument commands needed to execute the sequence. Gly -Q Manager
ships with several examples of instrument methods that can be modified and saved by the user.
To create or modify an instrument method, select the Instrument Method tab and pick one of the
existing instrument methods from the drop-down menu:
Instrument Method Tab
User Manual 35
Modify instrument commands for Calibration Ladder, Unknown Sample and End of Sequence steps by
selecting Action, High Voltage, Duration and Autosampler Position:
GU Ladder
Samples
Shutdow n
The following instrument commands can be used to create an instrument method. Click on the box in the
Action column in any row three times to bring up the pop-up menu below to select a command:
• High Voltage Purge: both high voltage and air pressure driven capillary purge
• Purge: air pressure only driven capillary purge
• Pause: pausing between steps
• Reagent Block Injection: injection from dedicated reagent wells and troughs on the autosampler
• Well Plate Injection: injection from a 96-well plate
• Separation and Detection: running the sample and collecting data
36 Gly-Q™ Glycan Analysis System
Detector Sensitivity Setting
By default, detector sensitivity is set to High for standard instrument methods. Sensitivity can be turned
down to either Medium of Low if saturated peaks are observed within the Processed Data Range, see
section 4.6 step 5.
Save the Instrument Method by clicking on Save or Save As.
Note: Instrument Methods that have already been used in a sequence cannot be overwritten and
can only be saved under a different name (Save As option).
4.8 Ending a Run
After samples have been processed, the system will return the Cartridge to the Park position (see
section 4.3, autosampler layout).
Use the “Load Sample” and “Load Reagents” buttons to remove sample plate and reagent tray.
Store the cartridge.
a. Remove the cartridge form the instrument and place tape over the cartridge cap (to cover the
pin hole). Return it to the original clamshell packaging. The cartridge tip must be in contact
with the gel block inside the package. Place inside the foil pouch and store vertically at room
temperature.
b. To store on the instrument: Press the Park button before shutting down the system. The
cartridge can remain on the system for up to 3 days. Fill the Park position of the buffer tray
(Section 4.3.3) with water to prevent the cartridge tip from drying during storage on the
instrument.
Samples may be stored, covered with sealing film, at -20°C for at least on month or up to 5 days at 4
°C.
User Manual 37
4.9 File Settings
File settings capture instrument serial number, cartridge and reagents lot information, define custom fields
on data reports, perform air and gel flow checks.
To update system settings, select the File tab:
Cartridge and reagents settings:
Instrument & software settings:
38 Gly-Q™ Glycan Analysis System
Account settings:
Data storage settings:
Note: This setting is for information only and cannot be changed.
Airflow check:
Gel Flow check:
User Manual 39
SECTION 5: CARE AND MAINTENANCE
Time Interval
Pr ocedure
Cleaning
Please clean the instrument with dry cloth
During Operation
Check the pressure on the software status bar to ensure that it is
between 45 and 60 psi.
Weekly
Check the condensation trap on the gel recharging air pump for
condensation. If there is condensation in the trap it should be
drained
• Turn off the power to the air pump
• Loosen the nut on the bottom of the condensation trap to
drain the water from the trap
• When the trap is empty, tighten the nut to seal the
condensation trap
• Turn on the power to the air pump; it will run briefly to
pressurize the system and then turn off.
Monthly
In addition to emptying the condensation trap as described above,
check the air filter:
• Turn off the power to the air pump
• Loosen the nut on the bottom of the condensation trap to
drain the water from the trap
• When the trap is empty, tighten the nut to seal the
condensation trap
• Check the air filter. If the filter is damaged or wet, use a
new filter to replace the old one. Replacement air filters
are supplied with the instrument and are available from
ProZyme.
• Turn on the power to the air pump; it will run briefly to
pressurize the system and then turn off.
• Turn the air pump on.
• Check the air flow using the Air Flow Check functionality
described in section 4.8, above.
40 Gly-Q™ Glycan Analysis System
SECTION 6: SYSTEM SPECIFICATIONS
General Technical Specifications
Environmental conditions
Operating temperature
Operating humidity
Operating altitude
20 to 30°C
40 to 95% RH, non-condensing
20 to 2000 m
Conditions of transportation and storage
Temperature
Humidity
-30 to +60°C
20 to 80% RH, non-condensing
UL installation category
Category II
Instrument Specifications
Input voltage
24 V DC 1.25 A Maximum
Output voltage
1-10 kV
Light source
LED (310 nm)
Fluorescence detector
Photomultiplier tube, A/D resolution 18-bit, long pass filter >385 nm
Computer connection
USB 2.0 or greater
Physical dimensions (L x W x H)
38 cm (L) x 30 cm (W) x 40 cm (H)
Weight
15 kg
Inlet Air Pressure
50 – 75 psi
Power Supply
SINPRO MPU32B-108
Power Supply Input Voltage
100 – 240 V AC, 47-63 Hz
Suggestion: Use a surge protector outlet for the instrument and the
computer to avoid electromagnetic interferences and damages to
the inner electrical devices.
Gel Recharging Air Pump Specifications
Input voltages
12 V DC 6.67 A Maximum
Output pressure range
50 – 60 PSI
Dimensions
16.5 cm(L) * 12.5 cm(W) * 10.5 cm(H)
Weight
1.4 Kgs
Power Supply
MEAN WELL GSM90B12-P1M
Power Supply Input Voltage
100 – 240 V AC, 47-63 Hz
Suggestion: Use a surge protector outlet for the instrument and the
computer to avoid electromagnetic interferences and damages to
the inner electrical devices.
User Manual 41
SECTION 7: WARRANTY STATEMENT
Limitation of Liability
Gly-Q Analyzer, software, and all related reagents are designed for the use of electrophoresis analysis in
general bio-chemistry laboratory for Research Use Only.
BEFORE ATTEMPTING TO OPERATE THE INSTRUMENT, READ ALL PRODUCT MANUALS AND FOLLOW THE
INSTRUCTIONS.
ProZyme assumes no liability whatsoever for any personal injury, property damage, or other loss resulting
from not complying or familiar with the manuals, or improper operation of the devices.
Warranty statement
ProZyme warrants all purchased products (other than extended warranties) against damage, defects in
materials or workmanship, and failure to conform to the Quality Specifications, for the period commencing
upon receipt of each purchased product by ProZyme Inc. through one (1) year after delivery of such
purchased product to ProZyme’s customers.
If, during the warranty period, any purchased product is discovered to be defective by reason of materials,
workmanship or failure to meet the Quality Specifications, please contact ProZyme Technical Support,
(800)457-9444 (US & Canada); +1 510-683-6900; info@prozyme.com
Terms and conditions of sale may be found at: http://www.prozyme.com/terms.html
42 Gly-Q™ Glycan Analysis System
SECTION 8: INSTRUCTIONS FOR DEPOT REPAIR RETURNS
To return the instrument for repairs, follow the steps below to clean surface and detached connectors and
tubing.
Open the cartridge door and ensure there is no cartridge in the instrument.
Check the sample and buffer tray to ensure there is no sample or fluid left in the instrument.
Turn off the power to the instrument and turn off the power to the gel recharging air pump.
To cut off the power disconnect the power plug to the instrument and the power plug to the gel
recharging air pump.
Unplug the USB cable in the back.
Unplug the power cable in the back.
Secure the cable node. Pull the connector header to unlock and detach the cable from instrument
Remove the air tubing by simultaneously pressing the connector and remove the tubing rapidly
Clean the outside of the instrument with dry cloth
Print and fill out the Decontamination Certificate located on the next page of this User Manual. Pack
the form with the instrument and contact ProZyme or your l ocal distributor for shipping details. The
User Manual is avai lable at http://prozyme.com/products/gq2100
User Manual 43
Decontamination Certificate
Please complete the form carefully and attach it to the item or instrument being returned.
Return authorization number
Company name
Contact person
Contact phone number
Ins trument model
Ins trument serial number
List accessori es returned with the instrument
No decontamination required
This instrument, and accessories if applicable, has not been in contact with any biol ogical,
chemical, or radioactive material that might cause infection or injury.
Decontamination required
This instrument, and accessories if applicable, has been in contact with biological, chemical, or
radioactive material and must be decontamina ted prior to return. Pl ease provi de details.
Material Yes/No Description
Chemical
Virus
Bacteria
Radi oisotope
Describe decontamination procedure:
I hereby certify that this instrument, and accessories if appl icable, is free of any biological,
chemical, or radioactive contamination.
Date:
Name:
Signature:
44 Gly-Q™ Glycan Analysis System
SECTION 9: FAQS
Q. Why does Gly-Q Manager not allow me to edit the Sequence Table I am preparing?
A. Be sure you have entered a Run Name before editing the Sequence Table
Q. Does the Gly-Q instrument require a minimum volume for analysis?
A. The Gly-Q instrument requires a volume of at least 30 µL in a 96 well plate well for a run.
Q. Gly-Q Manager does not seem to be communicating to the instrument. How can this be fixed?
A. Ensure that the USB cable is intact and installed correctly.
Ensure that the instrument is turned on.
If 1&2 above are confirmed, reboot the instrument and computer. Occasionally communication can be
lost if a prolonged period of inactivity is incurred.
Gly-Q Manager installs a Device Driver. If the driver is not installed properly instrument communication
will not occur. Check with your IT professional to insure your computer is configured to accept Device
Driver installation.
Q. What should I do about injection count warning or error messages?
A. The Gly-Q cartridges have both an expiration date and a limit on the number of injections that can be done
using each cartridge. When the cartridge is old or has been used for many injections the performance may
deteriorate. Cartridges have an absolute limit of 250 injections and a recommended limit of 200 injections.
Warning Message – Exceeding the Recommended Injection Limit of 200
In this case the run can be started but there it is possible that the cartridge performance will degrade during
the run. This is unlikely and in most cases the run will be completed successfully.
User Manual 45
Error Message – Exceeding the Absolute Injection Limit of 250
In this case the run cannot be started until you reduce the number of injections in the sequence.
Error Message – Cartridge has Expired
In this case you must use a different cartridge to perform the run.
Q. How do I remedy the “Cannot Get Cartridge Information” error message?
A. This message indicates that there is a problem reading the information on the cartridge RFID tag. In most
cases the system will allow you to enter the cartridge information manually (see section 4.4.1) but in this
case manual entry is no longer working. If this happens you must contact ProZyme technical support for
assistance.
Note: If this happens you will be able to use the system with any cartridge that has a working RFID tag.
Q. How do I remedy the “Low Pressure” error message?
A. Ensure that pump is turned on. If the pump is on then check that the airline connections are intact and
that the air filter is current and functional. The Airline Check in section 4.8 is another way to check this
parameter.
46 Gly-Q™ Glycan Analysis System
Q. The Air Pump runs quite frequently. Is this normal?
A. The air pump should run for ~ 30 seconds sporadically throughout an analysis session. If the pump is
running for greater than 1 minute regularly throughout the run this could be an indication of air flow
compromise. Again, the user should check integrity of airlines, air filters and perform the Air Flow function
described in Section 4.8, above.
Q. When is the Gel Flow Check function used?
A. The Gel Flow check in section 4.8 is used to insure gel flow in a cartridge is optimal. If a cartridge is stored
improperly the capillary may become clogged and consequently functionality may also be affected. The Gel
Flow Check can be used to determine presence of a potential clog. If a clog is detected the user is advised to
prime the cartridge as described in the cartridge preparation section, 3.6.2.
Q. Th e Lower Migration S tandard (LMS) and/or Upper Migration S tandard (UMS) were not found or aligned
correctly. What can I do?
A. Within the Data Tab, Sample window, expand the sample to list all peaks as shown in the illustration below.
Right click on the sequence that corresponds to the LMS/UMS and designate it as such. Gly-Q Manager
further helps facilitate this process by enabling visualization with the corresponding electropherogram in the
window above the Sample. Please see below for an example.
Manually designated LMS or UMS will be named accordingly in bold print, see below:
User Manual 47
Q. When collecting data, why can it not be saved in real time on a network or to a cloud location?
A. The system collects data in real time and is designed to save data on the local hard drive to prevent data
loss if the network or internet connections are down. Once data has been collected there are a number or
options available to move data to other computers. You can move data to a different computer running
Gly-Q Manager using the data export and data import functions using the QDF data file format. If you want
to analyze data using programs that support the industry standard AIA format such as Chromeleon or
Empower you can use the data export function with the CDF data file format. If you want to analyze data
using programs that support the CVS format such as Microsoft Excel, you can use the data export function
with the CVS data file format.
48 Gly-Q™ Glycan Analysis System
SECTION 10: LEGAL NOTICES
10.1 Trademarks & Tradenames
ProZyme, Gly-Q, Gly-X, N-Glycanase, and InstantQ are trademarks or registered trademarks of ProZyme,
Inc., in the United States and other countries. All other trademarks are the property of their respective
owners.
Failure of a mark to appear on this page does not mean that ProZyme does not use the mark nor does it
mean that the product is not actively marketed nor is not significant within its relevant market.
10.2 ProZyme Virtual Patent Marking
Visit http://www.prozyme.com/patents for a list of ProZyme products and patents.
User Manual 49
SECTION 11: RESOURCES AND REFERENCES
Visit ProZyme’s website for additional information, downloadable posters, publications and technotes.
http://prozyme.com/pages/resources
50 Gly-Q™ Glycan Analysis System
SECTION 12: TECHNICAL ASSISTANCE
ProZyme is committed to developing rapid, automatable methods for glycan analysis. Call us to discuss
products in development.
If you have any questions or experience difficulties regarding any aspect of our products, please contact us:
TOLL FREE (800) 457-9444 (US & CANADA)
PHONE (510) 638-6900
FAX (510) 638-6919
E-MAIL info@prozyme.com
WEB www.prozyme.com
ProZyme values customer opinions and considers customers an important source for information regarding
advanced or specialized uses of our products. We encourage you to contact us. We welcome your
suggestions about product performance or new applications and techniques.
User Manual 51
Trademarks and Tradenames. ProZy me, Gly -Q, Gly-X,
N-Glycanase, Gly-Q and InstantQ ar e trademarks or regi ster ed
trademarks of ProZyme, Inc., in the United St ates and other countr ies.
All ot her t rademark s are the property of their respective owners.
© 20 17-20 18 ProZyme, Inc. GQ2100 Version AF
www.prozyme.com
ProZyme, Inc. Headquarters
3832 Bay Center Place
Haywa rd, CA 94545
Toll Free: +1 (800) 457-9444
Phone: +1 (510) 638-6900
Email: info@prozyme.com
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