Before you start

This topic lists the required hardware, software, AssayMAP Starter Kit, labware, and reagents for running the In-Solution Digestion protocol. If you have questions about these items, contact Agilent Customer Service.

Hardware

Required hardware

 

 

The following figure and table show the components of the AssayMAP Bravo Platform, which is 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

 

Optional equipment

You might need the following when preparing the samples and reagents:

•	Microplate centrifuge, such as the Agilent Microplate Centrifuge or equivalent

•	Heated Incubator

•	Microplate sealer, such as the PlateLoc Sealer or equivalent

 

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Software

 

 

The following table lists the minimum software requirements:

 

Software	Version
Agilent VWorks Automation Control	13.1.5
Agilent Protein Sample Prep Workbench	3.2
Microsoft Excel Required for the reagent volume calculators and method setup tools.	2016

 

 

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Labware and starter kits

The In-Solution Digestion protocol works with a broad range of user-supplied reagents for denaturation, reduction, alkylation, and proteolysis steps. This protocol requires a specific set of labware that can be sourced from various vendors.

Labware required

The following table lists the labware required for the In-Solution Digestion: Multi-Plate application.

 

Labware	Part number
1.2-mL Deep-Well Plate (qty 2)	ABgene AB-1127
96-Well Round Bottom, White Plates (qty 11)	Greiner 650207
96-Well PCR Plate (qty 1)	Eppendorf 30129300
96 250-µL Pipette Tips (qty 1)	Agilent 19477-002

For details about the labware, see the Labware Reference Guide in the Literature Library page of the Protein Sample Prep Workbench.

Starter kits

Agilent offers starter kits for performing In-Solution Digestion and Peptide Cleanup, as these two applications are often performed sequentially. The following table lists the two starter kits that are available for In-Solution Digestion and Peptide Cleanup. Each starter kit contains both cartridges and labware.

 

Kit	Part number
AssayMAP Digestion and RP-S Cleanup Starter Kit— Contains 96 reversed-phase (RP-S) cartridges and Starter kit labware for In-Solution Digestion and Peptide Cleanup	G5496-60034
AssayMAP Digestion and C18 Cleanup Starter Kit— Contains 96 C18 cartridges and Starter kit labware for In-Solution Digestion and Peptide Cleanup	G5496-60013

AssayMAP cartridges

The following table lists the two cartridge types that are included in the starter kits.

You can purchase each of the cartridge types as an individual rack of 96 cartridges without the labware. To order the cartridges, contact Agilent Customer Service.

 

Cartridge type	Part number
AssayMAP C18 cartridge rack (Qty 96)	5190-6532
AssayMAP RP-S cartridge rack (Qty 96)	G5496-60033

A third type of cartridge, AssayMAP Resin-Free cartridge rack (G5496-60009), is not included in the starter kit, but can be used for mock runs or to fill remaining positions in columns that are partially occupied by the C18 and RP‑S cartridges, if necessary. For more information, see the Peptide Cleanup v2.0 user guide section on Preparing the samples.

Starter kit 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.

 

The following table lists labware that are included in the starter kits (G5496-60034 and G5496-60013).

Note: Additional labware are included in the starter kits but are required for the Peptide Cleanup application only. For more information, see Peptide Cleanup v3.0 User Guide.

 

Labware	Part number
1.2-mL Deep-Well Plates (qty 2)	ABgene AB-1127
96-Well Round Bottom, White Plates (qty 11)	Greiner 650207
96-Well PCR Plates (qty 3)	Eppendorf 30129300
12-Column Low-Profile Reservoirs (qty 4)	Agilent 201280-100
96-Well Round-Bottom, Clear Plates (qty 2)	Greiner 650201
250-µL Pipette Tips	Agilent 19477-002

For details about the labware, see the Labware Reference Guide in the Literature Library page.

 

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Reagents

The types and amounts of reagents required to prepare for the In-Solution Digestion protocol depends on a combination of factors, including specific chemistry requirements, the number of samples to process, and volumes and concentrations of reagents necessary to conduct denaturation, reduction, alkylation, and proteolysis. The In-Solution Digestion Reagent Volume Calculator manages this complexity by preparing a reaction summary, optimized solution recipes, and microplate layouts for all master reagents based on your input values.

For more information, see Preparing the reagents.

 

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