Search Linwei Li  2021-06-07

Hello Nick,
I tried search results using FragPipe and raw files. However, when I tried to import the search results in skyline, there is an error report showing that I need to have mzxml files instead for import.
I am not sure how to solve this. I think the reason is because I have run mzxml format files before and it saves the previous cached data. I am not sure if I need to remove previous cached data because they are from a separate skyline file. At the same time, I really need skyline to import raw files instead so that I can start a ion mobility library (if mzxml files are imported, ion mobility library will show no result.)
I have attached the error report below. Thank you so much!


Nick Shulman responded:  2021-06-07
That error message is rather confusing.

The thing that you need to understand about that error message is that "|" means "or".

So, the error message is saying that BiblioSpec tried to find a file whose named started with "2020-1-21-kb-70min_FAIMS_100micron_3cv_-35_-45_-55-OTIT_AJ-DMSO-1" and ended with one of the following filename extensions:
".mz5", ".mzML", ".mzXML", ".ms2", ".cms2", ".bms2", ".pms2", or perhaps even "_uncalibrated.mgf" or "_calibrated.mgf".

The error message is also telling you that it tried looking in the current directory (i.e. the same directory that had the pep.xml file in it), as well as the parent of the current directory (that is "..") or the grandparent of the current directory ("../..").

In order to build a spectral library from .pepxml files, you definitely do need to have some sort of mass spec data file (.mzML, etc), since the pepxml. Do you have any mzML (or other type) files? Can you copy them into the same folder as your pepxml files?

By the way, this is a very helpful page which tells you exactly which peptide search engines BiblioSpec understands, and which files you need to give to BilbioSpec in order to build a spectral library:

-- Nick
Linwei Li responded:  2021-06-07
Hi Nick,
I don't want to use mzxml files because they cannot yield results after I added the ion mobility library (picture on the right).
Therefore, I wonder if I can make skyline import raw files. Regarding what you said, "in order to build a spectral library from .pepxml files, you definitely do need to have some sort of mass spec data file (.mzML, etc), since the pepxml." Can I make the maxx spec data files raw files instead?
The issue I am having is that even if I searched with FragPipe using raw files, skyline still needs mzxml files when importing.
Thanks for replying. :)

Nick Shulman responded:  2021-06-07
BiblioSpec does not know how to read raw files.

It sounds like you are saying that FragPipe was able to search your raw files without them ever having been converted to .mzML.
If you want to build a spectral library from those search results, you should use ProteoWizard MSConvert to create .mzML files for BiblioSpec to use.

I am not sure that I understand what you are asking.
-- Nick
matt.chambers42 responded:  2021-06-07
BiblioSpec does know how to read RAW files...but only for certain identification formats. Each id format (pepXML, mzIdentML, proxlXML PrideXml, etc.) has a different set of supported spectrum formats. MzIdentML input supports reading from vendor files, but pepXML does not. I don't think there's a good reason for this. I should be able to add support for vendor formats in pepXML.
matt.chambers42 responded:  2021-06-07
Heh, looks like I messed up with that Blib formats table. It says MSFragger input supports RAW spectrum files. Oops.
matt.chambers42 responded:  2021-07-09
MSFragger input and pepXML input in general should support vendor spectrum files (RAW, .d, .WIFF, .lcd) in the next daily.