Apply standard procedures

My proteomics assay is a bit more complex. I’m honestly not a proteomics expert and I would not know how to annotate this in detail myself. It is based on mass spectrometry and routinely performed at our proteomics facility.

For the proteomics assay, we’ll apply standard operating procedures (SOPs) to sample records provided by a proteomics facility.

Add Proteomics Assays and apply SOPs

Section titled Add Proteomics Assays and apply SOPs

Follow the same steps as before to add two assays and sort the available demo data.

Proteomics – Mass Spectrometry

Section titled Proteomics – Mass Spectrometry

ARCitect

1. Create an assay Proteomics_MS.
2. Import the assay files and folders from the demo data into the assay. Use the “Import Files” and “Import Directories” functions accordingly:

Loading diagram...

Source

flowchart LR
subgraph d[Demo Data]
    D1@{ shape: docs, label: MS_Raw}
    D2@{ shape: doc, label: AssayTemplate_Proteomics_MS.json}
end
subgraph a[ARC]
    A1@{ shape: lin-cyl, label: Proteomics_MS/dataset/}
    A2@{ shape: lin-cyl, label: Proteomics_MS/protocols/}
end
D1 --> A1
D2 --> A2
classDef sub fill:#FFFFFF,color:#2d3e50,font-size:1.1em;
class d,a sub;
classDef item font-size:0.9em;
class D1,D2,A1,A2 item;

Load the data annotation into the respective annotation tables

1. Create a new annotation table for the assay Proteomics_MS.
2. In the bottom-right corner click < to open a panel on the right.
3. On top of the panel, navigate to the templates tab.
4. In the “Add template(s) from file” section, select ARCtrl and click Upload protocol.
5. Navigate to and select the file AssayTemplate_Proteomics_MS.json and click open.
   • Select the “Import Type” ..With Values
   • Check the Import boxes
   • Click Submit

Proteomics – Data analysis

Section titled Proteomics – Data analysis

Repeat the same for the “Proteomics Data Analysis” files.

ARCitect

1. Create an assay Proteomics_DataAnalysis.
2. Import the assay files and folders from the demo data into the assay
3. Create suitable annotation tables and import the data annotation, respectively.

Loading diagram...

Source

flowchart LR
subgraph d[Demo Data]
    D1@{ shape: doc, label: combined_protein.fasta}
    D2@{ shape: doc, label: MSFraggerOutput/combined_protein.csv}
    D3@{ shape: doc, label: AssayTemplate_Proteomics_DataAnalysis.json}
end
subgraph a[ARC]
    A1@{ shape: lin-cyl, label: Proteomics_DataAnalysis/dataset/}
    A2@{ shape: lin-cyl, label: Proteomics_DataAnalysis/protocols/}
end
D1 --> A1
D2 --> A1
D3 --> A2
classDef sub fill:#FFFFFF,color:#2d3e50,font-size:1.1em;
class d,a sub;
classDef item font-size:0.9em;
class D1,D2,D3,A1,A2 item;