About the Workflow Library

The Workflow Library is a collection of protein sample preparation workflows. Each workflow consists of a set of applications that are performed in sequence to complete an experiment. In addition, the workbench contains links to utilities that facilitate sample and reagent preparation, the transition between applications, and the transition between the output of the final application and the input of the analytical instrument.

 

General Workflows

 

Workflow	Description
Affinity Purification	Creates custom affinity cartridges and uses them to enrich target molecules. The workflow consists of the following applications: • Immobilization. For details, see the Immobilization v2.0 User Guide. • Affinity Purification. For details, see the Affinity Purification v2.0 User Guide.
Peptide Sample Prep	Digests proteins, then desalts the peptide resulting from the digestion, and optionally fractionates the peptide mixture. The workflow consists of the following applications: • In-Solution Digestion. For details, see the In‑Solution Digestion: Single Plate v1.2 User Guide. • Peptide Cleanup. For details, see the Peptide Cleanup v3.0 User Guide. • Fractionation. For details, see the Fractionation v1.1 User Guide.
Rapid Antibody Digestion	The workflow consists of the following applications: • In-Solution Digestion. For details, see the In‑Solution Digestion: Single Plate v1.2 User Guide. • Peptide Cleanup. For details, see the Peptide Cleanup v3.0 User Guide. • Protein Cleanup. For details, see the Protein Cleanup v2.0 User Guide.

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Post-Translational Modification Workflows

 

Workflow	Description
Phosphopeptide Enrichment	Digests proteins, then desalts the peptide resulting from the digestion, and enriches the phosphopeptides. The workflow consists of the following applications: • In-Solution Digestion. For details, see the In‑Solution Digestion: Single Plate v1.2 User Guide. • Peptide Cleanup. For details, see the Peptide Cleanup v3.0 User Guide. • Phosphopeptide Enrichment. For details, see the Phosphopeptide Enrichment v2.1 User Guide.
N-Glycan Sample Prep	Purifies glycoproteins, normalizes the glycoproteins, and releases, labels (2AB, APTS, or instantAB) and cleans glycans. The workflow consists of the following applications: • Affinity Purification • Normalization • N-Glycan Sample Prep, RX Digestion & 2AB Labeling. • N-Glycan Sample Prep, RX Digestion & APTS Labeling. • N-Glycan Sample Prep, RX Digestion & InstantAB Labeling. • N-Glycan Sample Prep, RX Digestion & InstantPC Labeling. You can access the instructions for these steps in the workflow from the N‑Glycan Sample Prep Workflow Navigator in the workbench.

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Accessing a workflow

To access a workflow:

1	In the Protein Sample Prep Workbench, do one of the following:

•	If you have not yet logged in, click Workflow Library. The VWorks software starts, and then the User Authentication dialog box opens.

 

Type your VWorks user name and password, and then click OK. The Workflow Library opens.

•	If you have already logged in to the software, click the Workflow Library button in any of the other libraries of the Protein Sample Prep Workbench.

2	In the Workflow Library, click the name of the workflow you want to use, and then click Open.

 

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