Using MudPIT in Scaffold Analyses

What does MudPIT mean?
MudPIT (Multidimensional Protein Identification Technology), developed by John Yates, ( is a way of analyzing spectra coming from two or more datasets each derived from the same biological sample. Using MudPIT considers all of the data to have come from one biological sample and treats it as such. If you analyze your data as MudPIT you will not be able to view peptide or protein analysis from individual MS samples.

When would I check the MudPIT checkbox?
You would want to check the MudPIT checkbox when your experimental parameters separate peptides, not proteins. A MudPIT analysis (also known as "Shotgun Proteomics") lumps all MS samples into one biosample, and reports the results for the entire biosample.

A MudPIT analysis differs from a Biosample analysis in that a peptide from any MS sample in the MudPIT can be combined with a peptide from any other MS sample in the MudPIT to form a protein. Also, when viewing a MudPIT sample in Scaffold's “Samples” view you cannot view individual MS samples.

For example:
If you collected two blood samples, digested the proteins in each sample with trypsin, and ran the digested proteins through LC-MS/MS (in multiple LC-MS runs), you would want to check the MudPIT analysis checkbox.

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