Can you send us the .csv file that you exported from Skyline?
I cannot tell from whether what you are seeing in your Excel spreadsheet is caused by something Skyline did wrong, or whether Excel is misinterpreting a valid CSV file.

I see that your report had columns "Times" and "Intensities" in it.
When you export that to either CSV or Tab-separated-values, a list of numbers like that is represented as a quote character followed by a comma-separated list of numbers followed by another quote character. Outside of those two quote characters will either be a tab character which Excel will interpret as a new column in the spreadsheet.

I see that at line 422 of your spreadsheet, it looks like the intensities, instead of appearing in the "intensities" column are in the first Excel column. I would need to see the original csv or tab-separated-value file to know why Excel did that. It might be that there is a maximum line length that Excel can handle, and that is what happens if a single line in the text file is more than that.

Also, if you would like, you can send us your report definition and your Skyline document.

An easy way to include the report definition in the Skyline document is to go to:
Settings > Document Settings > Reports
and check the checkbox next to the report you were looking at.

Then, you can use the menu item:
File > Share
to create a .zip file containing your Skyline document which will also include that report definition.

If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url
-- Nick

Hi Nick,

The Table exported by skyline is attached, which is used the following way. File > export > Chromatogram
 
Best regards,

Twinnie

Thank you for sending that TSV file.
I see that on line 422, in the middle of what is supposed to be a list of numbers, there is a quotation mark, a line break, and then the list of numbers continues on the next line, and ends with the quote that it's supposed to have, and then there are a bunch of tabs which presumably make up for the missing columns on that line that should not exist.

Are you sure that that is the file that you got when you exported chromatograms from Skyline? From looking at the code, I cannot see how Skyline could produce something like that.

Can you send us your Skyline document? In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:
https://skyline.ms/files.url

By the way, there is another way to see chromatogram data using the Document Grid and/or File > Export > Report
If you edit the report, there are a couple of chromatogram data columns under:
Proteins > Peptides > Precursors > Transitions > Transition Results > Chromatogram

-- Nick

Hi Nick,

Yes, this table was exported by Skyline via the Chromatogram option. And those chromatogram data columns under you mentioned way were not what I wanted. I want to get the matrix that could draw precursor XIC profiling.

The skyline.zip file is uploaded which contains two peptides one of which is not garbled, the other one appears garbled. https://skyline.ms/files.url
The .tsv file is attached and which exported by the skyline.zip file as follows. File > export > Chromatogram.

Winnie

The file that you have attached, "Skyline_2peptides.tsv" looks fine to me. I do not see any line breaks where they are not supposed to be.
Do you see something wrong in that file?
-- Nick

Hi Nick,

I want to make our communication more efficient which is limited by the time difference between us. I am living in China. Which country do you live in? I can match your time at your convenience. Thanks!

Winnie

Hi Nick,

The screenshot is attached. The 7th row of this table appears garbled.

Winnie

That's not what it looks like when I open that .tsv file in Excel. Here is a PowerPoint showing what I am seeing.

I have seen some web pages on the Internet which say that Excel does not allow more than 32767 characters in a single cell. Maybe that limit is causing you problems.
https://excel.tips.net/T003163_Character_Limits_for_Cells.html

I'll be awake for another 3 hours tonight if you have more questions. I wake up again another 8 hours after that.
-- Nick

Hi Nick,

I have resolved the issue of the 2peptides.tsv file with your suggestion. Another question, there are 100 peptides that we are interested in. The tsv file named R01_20220207_skyline is exported by skyline file which contains 100 peptides from one raw file. The skyline zip file and the 2 peptides.tsv I shared are just example data that were generated by deleting 98 peptides for convenience. Acutually, I need to export 100 peptides chromatogrm from ~200 raw files. The .tsv with 100 peptides chromatogrm from ~200 raw files about 4 GB in size. It seems impossible to convert this table by excel. Did you have any suggestion for this issue?

Winnie

Whenever I have to look at text files which are more than a few gigabytes, I use a program called "EmEditor". You can download program that from here:
https://www.emeditor.com/
The web page says that the premium edition of EmEditor even understands CSV files, but I have never used that feature.

If you want to write your own program to read the exported chromatogram data, I know that some people have had success using the R programming language. The Skyline external tool "AvantGardeDIA" was written in R and reads chromatogram data which is exported using a Skyline report.
-- Nick

OK, I will try both ways you suggested and update the progress tomorrow.

Hi Nick,

I am glad to tell you that I have resolved the garbled tsv. file by Python. Thanks a lot.

Winnie