CSV File Creation
The Samples-protein input tab in the Project Creation window of an Intact workflow provides users with the ability to add multiple sequences or sequence combinations and associate them to a list of files. A .csv file needs to be populated in advance with the following structure:
| ColumnName | FilePath | Sample Name | Sequence or Protein Name 1 | Sequence or Protein Name 2 |
| Expectation | Desired or Undesired | Desired or Undesired | ||
| ColumnType | SampleName | Mass | Mass | |
| C:\ExamplePath | Example Sample Name | Sequence1 |
Sequence2 |
The disulphide count is defined after the sequence. If all possible disulfide bridges shall be considered, no additional definition is needed. The definition of the disulphide count is always at the end of the sequence or sequence combination as shown in this example:
Sequence combinations are separated with a comma, which can conveniently be created in Excel as shown in this example:
Each additional sequence or sequence combination is an additional column. A sequence name or sequence combination can only be assigned to a single file as shown in the example below:
Alternatively, instead of defining the sequence, masses as numeric values can be used directly. A mixture of sequences and masses can be used as well, for cases to define a fixed modification of a protein as shown in the example below:
Metadata Input
In addition to sample and sequence information, the user can add metadata as well within the .csv file. The added metadata is visible in the Project table of the Analysis view and as fields that can be dragged and dropped in the report. The ColumnType for a meta data field is SampleName. Values in the ColumnName and the ColumnType rows must be different as shown in the example below:
CSV Template Creation
Templates for .csv input files can be created within the Byos inspection view of an existing project. After clicking File > Export > Generate MS path template CSV, a window will pop up. Definition of a path is that contains raw data files is required. Enabling the recursive search will list all MS raw files within the hierarchy of the selected file. By clicking the Save button the CSV file can be locally stored.
Workflow Creation
The created .csv file can be imported in the Samples-protein input by clicking Import CSV:
After selecting a .csv, file a table shows up with the information contained in this file:
The samples are populated accordingly in the Samples table:
The sequences and sequence combinations associated to the single files are populated as well: