Before you start
This topic lists the required hardware, software, AssayMAP cartridges, labware, and reagents for running the Peptide Cleanup: Aspiration Mode protocol. If you have questions about these items, contact Agilent Customer Service.
Hardware
The following figure and table show the components of the AssayMAP Bravo Platform, which are required for running the AssayMAP protocols.
Figure AssayMAP Bravo Platform components
 |
Item | Required hardware |
|---|---|
1 | Gripper upgrade |
2 | Bravo 96AM Head |
3 | 96AM Wash Station or the later model 96 Channel Wash Station |
4 | Pump Module 2.0 and two carboys |
5 | 96AM Cartridge & Tip Seating Station |
6 | Risers, 146 mm |
7 | STC controller |
8 | Peltier Thermal Station with custom plate nest |
9 | Thermal plate insert |
10 | Orbital Shaking Station with Control Unit |
To avoid a hardware crash and equipment damage, ensure that the wash station contains the white wide-bore chimneys when using the 25 µL cartridges. Note: The white wide-bore chimneys work for both 5-µL and 25-µL cartridges and are standard on wash stations purchased in 2020 onward. The wide-bore chimneys are white plastic, whereas the standard-bore chimneys are a semi-clear plastic. For details, see the 96 Channel Wash Station Maintenance Guide.
Note: The 25-µL have not yet been optimized on the Peptide Cleanup: Aspiration Mode application. If you are interested in trying them on this application, contact Agilent Customer Service for advice.
Optional equipment. You might need the following when preparing the samples and reagents:
• Microplate centrifuge, such as the Agilent Microplate Centrifuge or equivalent
• Microplate vacuum concentrator for concentration and drying of samples
• Microplate sealer, such as the PlateLoc Sealer or equivalent
Software
The following table lists the minimum software requirements.
Software | Version |
|---|---|
Agilent VWorks Plus (compliance-enabled edition) or VWorks Standard | 14.4 |
Agilent Protein Sample Prep Workbench | 4.0.2 |
Microsoft Excel Required for the reagent volume calculators and method setup tools. | Microsoft Office 365 32-bit edition |
For an overview of the software components, see Overview of software architecture.
AssayMAP cartridges
The following table lists the available AssayMAP cartridges for performing Peptide Cleanup on the AssayMAP Bravo Platform. Each cartridge type can be purchased as a rack of 96 cartridges.
Note: This application has not yet been optimized for the 25 µL cartridges.
Cartridge type | Part number |
|---|---|
AssayMAP Reversed-Phase (C18) cartridge rack | 5190-6532 |
AssayMAP Reversed-Phase (RP-S) cartridge rack | G5496-60033 |
AssayMAP Resin-Free cartridge rack This cartridge can be used for mock runs or to fill remaining positions in columns that are partially occupied by the C18 and RP-S cartridges. For details, see Preparing the samples. | G5496-60009 |
For more details about the available cartridges, see the Agilent AssayMAP Bravo Cartridges Selection Guide or the AssayMAP Cartridges page on Agilent.com.
Cartridge use and storage guidelines
See the cartridge box label for storage guidelines.
Follow these guidelines to get the best performance from AssayMAP cartridges:
• Use only primed and equilibrated cartridges.
Cartridges ship dry and, therefore, contain air entrained in the resin bed. Failure to prime the cartridges can prevent the reagents and buffers from accessing parts of the resin bed, resulting in reduced capacity and poor reproducibility.• Do not allow wetted cartridges to dry out.
Note: Cartridges will not dry out during the course of a normal application run. Cartridges can dry out if they are exposed to air for extended periods (e.g., >1 hour) after they have been primed and equilibrated.
If you need to store primed and equilibrated cartridges for a short period, ensure that you use the lidded blue rack-receiver plate stack with an appropriate solution in the receiver plate chimneys such that the cartridge tips are submerged in the solution.
• AssayMAP cartridges are intended to be single-use consumables. Agilent does not provide a performance guarantee for cartridges that have been used more than once.
Starter kits
The following table lists the two starter kits that are available. Each starter kit contains both cartridges and labware.
Starter Kit | Part number |
|---|---|
AssayMAP Digestion and RP-S Cleanup Starter Kit— Contains 96 Reversed-Phase (RP-S) cartridges and Labware for In-Solution Digestion: Multi-Plate and Peptide Cleanup. | G5496-60034 |
AssayMAP Digestion and C18 Cleanup Starter Kit— Contains 96 Reversed-Phase (C18) cartridges and Labware for In‑Solution Digestion: Multi-Plate and Peptide Cleanup. | G5496-60013 |
The following table lists labware that are included in the Peptide Cleanup Starter Kit.
Note: The labware included in the starter kits are for both the Peptide Cleanup: Aspiration Mode and the In-Solution Digestion applications. For the Peptide Cleanup: Aspiration Mode labware requirements, see Labware. For the In-Solution Digestion: Multi-Plate labware requirements, see In‑Solution Digestion: Multi-Plate v2.0 User Guide.
Labware | Part number |
|---|---|
1.2 mL Deep-Well PolyPro Clear Plates (qty 2) | ABgene AB-1127 |
96-Well U-Bottom PolyPro White Plates (qty 11) | Greiner 650207 |
250-µL Pipette Tips (qty 1) | Agilent 19477-02 |
12-Column Low-Profile Reservoirs (qty 4) | Agilent 201280-100 |
96-Well Round-Bottom, Clear Plates (qty 2) | Greiner 650201 |
96-Well PCR Plates (qty 3) | Eppendorf 30129300 |
Labware
Labware requirements vary depending on experimental design. The following table provides a complete list labware options and the corresponding deck locations.
The following figure shows the nine Bravo deck locations for labware.
Use only the labware specified for each deck location. Using different labware or placing labware at unapproved deck locations can cause a collision resulting in equipment damage.Figure Labware locations on the Bravo deck (top view)
 |
Labware | Manufacturer part number* | Deck location options |
|---|---|---|
12 Column, Low Profile Reservoir, Natural PP | Agilent 201280-100 | 3, 5–8 |
8 Row, Low Profile Reservoir, Natural PP | Agilent 201282-100 | 5–8 |
96 ABgene 1127, 1mL Deep Well, Square Well, Round Bottom | ABgene AB-1127 | 3—8 |
96 Eppendorf 30129300, PCR, Full Skirt, PolyPro | Eppendorf 30129300 | 4, 7, 9 |
96 Greiner 652270, PCR, Full Skirt, PolyPro | Greiner 652270 | 4, 7, 9 |
96 Greiner 650201_U-Bottom, Clear PolyPro | Greiner 650201 | 3—9 |
96 Greiner 650207_U-Bottom, White PolyPro | Greiner 650207 | 3—9 |
96 Greiner 675801, Half Area, Flat-Bottom, UV Star | Greiner 675801 | 4, 7, 9 |
96 V11 Manual Fill Reservoir | Agilent G5498B#049 | 5–8 |
*For dimensionally equivalent alternatives and other labware details, see the Labware Reference Guide in the Literature Library page of the Protein Sample Prep Workbench. | ||
Reagents
The volume, type, and concentration of reagents required for peptide cleanup vary depending on sample characteristics and the desired analytical result. Consult published literature for reagent recommendations for sample and surface chemistry combinations. See the Agilent AssayMAP Bravo Citation Index for published papers that use the AssayMAP Peptide Cleanup application.
By default, the syringes are rinsed thoroughly with deionized water at the wash station after completing the protocol to reduce the risk of premature syringe failure. To perform more stringent syringe washing between runs, use the Syringe Wash utility. For details, see Syringe Wash v3.0 User Guide.
All labware require volume overage for the protocol to execute properly. Use the Reagent Volume Calculator to determine volume requirements for specific protocol conditions. See Preparing the solutions.