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The number of unique peptides is more than the number of total peptides

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The number of unique peptides is more than the number of total peptides smisra1  2013-03-08 08:43
Status: Closed
 
Hello all,

    I am new to CPAS and trying to understand the system. I have few questions-

1- When I exported the table of ProteinProphet (legacy) view, I notice that for many of the proteins the number of unique peptides is more than the number of total peptides. Why?

2- I am using large dataset and My exported table (excel) is limited by 65,536 rows. I am using excel 2007, so this should not be the case. ow to export so that I have the full list of the proteins/peptides.

3- What is the difference exactly in "protein group" and "proteinProphet(legacy)" under grouping section.

It would be great if somebody can provide me answers to these questions.

Thanks

Sandeep Misra
 
 
jeckels responded:  2013-03-11 17:03
Hi Sandeep,

1. When viewing ProteinProphet data, we use the unique and total peptide counts that are generated by ProteinProphet and are part of the protXML file. Therefore, this is probably a question that is best answered on the TPP forums. I typically see this for low-confidence protein group assignments, where the probability is 0.

2. Unfortunately the MS2 export currently creates a .xls file, which is limited to 65,536 rows. I'd love to add support for existing .xlsx files which support many more rows, but it's not currently on any of our customers' priority lists. You can also export to TSV, which won't have the row limit, and load that file in Excel 2007 or newer.

3. The "Protein Group" grouping shows protein information as child rows under each protein group, but doesn't show peptide data. The ProteinProphet views (both legacy and the ProteinProphet view under the Standard grouping) show peptides as child rows. In either type of view, you can filter on columns in the child rows, but you can't filter on protein criteria (gene symbol or mass, for example) in the ProteinProphet views.

Thanks,
Josh