Inter v. Inter_combine results

[Elizabeth Chang]

Hi everyone,

pLink gives us so many different Excel spreadsheets as results and I’m not sure which one to use.  When it has a “_combine” in the filename, what does that mean?  For example, what is the difference between "sample1_inter.peptide.xls" and “sample1_inter_combine.peptide.xls?” For some more background, I set up my search for my inter-links and I thought that the two spreadsheets would be the same.  However, there are some peptides that were not listed in the other spreadsheet.

If anyone has some insight on the different formats for the results and thoughts on which one is the most accurate/best, please share!

Thanks,

Elizabeth Chang

[Bing]

Hi Elizabeth,

Sometimes, I am also confused about this. Previously, I know what is the difference between them, but I totally forgot it now. I always use .xls file from 1.sample/search/HCD_inter. It should be correct. I will contact with pLink developer about this question. When I get the answer, I will let you know.

Best regards

Bing Yang

[Michael Riffle]

Wanted to follow up on this, as I'm running into the same questions.

After splitting a MGF file into many files and running an analysis, I have these two directories (in addition to an _inter) directory for each MGF file):

"myfile_inter/"

"myfile_inter_combine/"

The first has a "myfile_inter.spectra.xls" file.

The second has a "myfile_inter_combine.spectra.xls" file.

These two files are not the same--what are they? Which one should be used? It sounds like "myfile_inter/myfile_inter.spectra.xls" is the one that should be used?

[Michael Riffle]

In following up to myself, it looks like the "myfile_inter_combine.spectra.xls" is the one actually used in the Plink HTML report--so I'll just go with that.