Once the job for MSstats work is done, you can submit this result by MSstats as a reanalysis in the MassIVE.quant. It is similar as Submit Quant Reanalysis, except that you can import the result of MSstats from the finished job.
3.1 Select Dataset
First, go to the webpage for the dataset you reanalyzed. You can search dataset MSV ID or PXD ID in dataset's web page.
Click the Add Reanalysis button:
3.2 Workflow Selection and Reanalysis Metadata Sections
Add Reanalysis button brings you to a MassIVE reanalysis attachment workflow input form.
At this point, the option 'MassIVE Dataset: Add Reanalysis Results' should be automatically selected in the
Workflow. Information regarding
Post-Translation Modifications should also be filled automatically, based on the original submission. You should add
- the title in
Title(at least 30 characters)
- the description for this reanalysis in
Description(at least 50 characters)
Example of a
Title: 'MassIVE.quant reanalysis from MaxQuant+ MSstats workflow from RMSV000000249.2'
Example of a
Description: 'MassIVE.quant reanalysis of data from the iPRG2015 study (dataset MSV000079843) using Andromeda for identification and MaxQuant for quantification(from RMSV000000249.2), followed by MSstats for statistical analysis of differentially abundant proteins. Here MSstats workflow was used.'
3.3 Reanalysis File Selection section
You should select all the files for your reanalysis in this section. Please go through both 3.3.1 and 3.3.2 below.
3.3.1 New files generated by MSstats workflow
MSstats workflow generates:
- CSV file for the result of differential abundance analysis from MSstats
- R script that is used for MSstats, based on your selection of options in the MSstats workflow
- The log file that is generated by MSstats, which records the version of R, MSstats, and parameters
You can select all three of them.
- Click '+' sign in front of Select Input Files from MassIVE Workflows Results option. Then, the job with the title that you wrote in the MSstats workflow will be shown.
- Click the
Selectbutton at the very right of this row.
Then, the new pop-up window,
File Selection, shows all files generated by MSstats. Let's select the file for the result of statistical analysis, first:
- Find the CSV file suffixed differential_abundance_analysis. For this example, the second row is for the result of statistical analysis.
- Select Statistical Analysis of Quantified Analytes from the drop-down button in the
- Click the
Addbutton at the very right in that row.
Repeat the same steps for the other three files.
- script.r and msstats.log should be in Methods and Protocols.
- summary_of_differentially_abundant_proteins.csv can be in Statistical Analysis of Quantified Analytes.
Finally, click the
Close button at the bottom-right on the pop-up window.
3.3.2 Quant files and Metadata used for MSstats workflows
Next, you should select all quantification file(s) used for MSstats workflow. This step is the same as for MSstats workflow. Please repeat the same steps that you did for the MSstats workflow. (The section 2.2. File Inputs in Step2-MSstats Workflow)
!! NOTE: To browse the dataset in MassIVE.quant, the three categories, 1) Quantification Results, 2) Metadata, 3) Statistical Analysis of Quantified Analytes, should have the file(s).
3.4 Reanalysis Container Selection section
The reanalysis attachment workflow will determine which source datasets were reanalyzed, and will then prepare what's referred to as a "reanalysis container" for your attachment. A reanalysis container simply refers to the unique set of datasets that were reanalyzed - usually only one, but possibly more. The workflow then attaches your results to this container. Any other reanalysis results attached (by any user) to this same set of datasets will also go in the same container.
Reanalysis Container shows all containers for the source dataset. You can choose one of them or make New reanalysis container. If you select New reanalysis container, then you should put the title for this container in
Reanalysis Container Title.
3.5 Workflow Submission section
Finally, you are ready to submit. Please type your email to get notice of the progress of the submission and click the Submit button.
Then, you will be redirected to a new page, which shows the progress. Please wait. It will take a few minutes.
After the job is done, the status will say 'DONE' and you will get the notification email.
Now this reanalysis is submitted and available under the dataset (For this example, MSV000798430). New RMSV ID is assigned for this analysis, RMSV00000000248.34. You can access all files (Please check Access Quant Reanalysis)