How can I use the MD Format to upload my data?

Regardless of the format of your quantitative data, you can now upload it to Mass Dynamics using the MD Format.

1. Login to app.massdynamics.com
2. Click on 'Create an experiment'
   
   
3. Choose "Choose Files" or "Choose Folder" depending on how your files are stored
   
4. There are 2 files that are needed. Do not be concerned with the name of each of the file, as we will detect the data in the files based on the the column names. For example, your file names could be called Protein_intensity.tsv and Peptide_data.tsv. Please ensure each of your files contains your data in the following structure.
   
   Example File: Protein_intensity.tsv
   
   

   Column Name	Notes
   ProteinGroupId (Primary key)	Mandatory i.e. `1` Needs to be a unique identifier for the protein group and only one value per sample per protein group Has to be an integer
   ProteinGroup	Mandatory i.e. `P12345;P23456` Needs to be a unique identifier for the protein group and only one value per sample per ProteinGroupId Multiple Ids separated by `;`
   ProteinNames	Optional i.e. `NBPF8_HUMAN;NBPF9_HUMAN;NBPFA_HUMAN` Multiple names separated by `;`
   GeneNames	Mandatory i.e. `NBPF10;NBPF19;NBPF20` Multiple names separated by `;`
   Description	Optional i.e. `Neuroblastoma breakpoint family member 19;Neuroblastoma breakpoint family member 20` Multiple descriptions separated by `;`
   SampleName	Mandatory i.e. `sample1` Name of the sample (can be the filename) Has to be a string Only one value per sample
   ProteinIntensity	Mandatory i.e. `1000` Normalised intensity values for each protein in the group in each sample
   Imputed	Mandatory i.e. `TRUE/FALSE` or `1/0` Imputed values for each protein in the group in each sample

    
   Example File: Peptide_intensity.tsv
   

   The peptide table is a table of intensities collapsed at the level of the modified sequence. One peptide that was detected in two charge state forms would be represented as one row per sample in the peptide table.

   Column Name	Notes
   ModifiedSequence (Primary key)	Mandatory i.e. `AAAC(UniMod:4)TTLGQMATDFAPNFQK` Modified sequence of the peptide
   StrippedSequence	Mandatory i.e. `AAACTTLGQMATDFAPNFQK` Stripped sequence of the peptide
   Unique	Mandatory i.e. `TRUE` TRUE if the peptide is unique to the protein group
   ProteinGroup	Mandatory i.e. `P12345;P23456` Needs to be a unique identifier for the protein group and only one value per sample Multiple Ids separated by `;` Has to be the same as in the protein intensity table A protein group in the peptide table may not be present in the protein table if the protein group is not quantified or if a protein group is made up of only nonunique peptides
   ProteinGroupId	Mandatory i.e. `1` Needs to be a unique identifier for the protein group and only one value per sample per protein group Has to be an integer Has to be the same as in the protein intensity table A ProteinGroupId in the peptide table may not be present in the protein table if the protein group is not quantified or if a protein group is made up of only nonunique peptides
   OtherProteinGroupIds	Optional i.e. `2;3` In the case of a nonunique peptide, the other protein group ids that the peptide is associated with
   ProteinNames	Optional i.e. `NBPF8_HUMAN;NBPF9_HUMAN;NBPFA_HUMAN` Multiple names separated by `;`
   GeneNames	Mandatory i.e. `NBPF10;NBPF19;NBPF20` Multiple names separated by `;` Has to be the same as in the protein intensity table
   Description	Optional i.e. `Neuroblastoma breakpoint family member 19;Neuroblastoma breakpoint family member 20` Multiple descriptions separated by `;`
   SampleName	Mandatory i.e. `sample1` Name of the sample (can be the filename) Has to be a string Only one value per sample Has to have the same number of samples and the same as the values reported in the protein table
   PeptideIntensity	Mandatory i.e. `1000` Normalised intensity values for each protein in the group in each sample
   Imputed	Mandatory i.e. `TRUE/FALSE` or `1/0` Imputed values for each protein in the group in each sample

5. After choosing the relevant files to upload for your file system, click "Next"
   
   
   
   
6. Mass Dynamics should now detect that it is the MD Format that you are using, and will detect the number of files found.
   
   
   
   
7. You can now either create your own Experiment Design or you can upload your own populated template
   
   
   
   
8. Go ahead and enter your Experiment Name and Experiment Description
   
   
   
   
9. Click "Create Experiment" and wait until your files upload
10. Get started with analyzing your data!