Orbitrap library

Orbitrap library MS-SZAOmics  2022-11-28
Hi I'm Merve and I'm very very new in Skyline. We have an Orbitrap (Exploris240). I wanted to study with my data on Skyline but I couldn't find a library for Orbitrap. As a beginning I started with BSA analysis. In library site like NIST, I guess there isn't a BSA library for Orbitrap. I'll be glad if you can help me about this issue.

Many thanks,
Nick Shulman responded:  2022-11-28
Any spectral library will probably work fine. You do not need to have a library that is specific to the type of instrument that you are using. Peptides behave very similarly across many types of instruments, and if you know which fragments are likely to be seen on one type of instrument, most of those will also be able to be able to be detected just as well on another type of instrument.

Skyline uses spectral libraries to decide which fragments (transitions) are likely to be seen, as well as which peptides.

Spectral libraries would be very useful if you were planning on collecting data on a triple quadrupole instrument, since you would need to tell the instrument which transitions to look for ahead of time.
But, with an Orbitrap, you can use much more simple methods.

Have you already collected any data on your Orbitrap? A common thing to do with an Orbitrap is "Data Dependent Acquisition" (DDA) where you do not tell the mass spectrometer what to look for. Instead, the mass spectrometer collects MS1 spectra, and then looks at the MS1 spectrum, sees which m/z's are most intense, and then collects a MS2 spectrum by fragmenting each of those intense m/z's.
Then, once you have your raw file, you can use a peptide search engine to figure out what peptides were in those MS2 spectra.
Typically, the thing that you need to provide to the peptide search engine would be a FASTA file, which would have a list of the proteins that you want to look for, or believe might be in the sample.

You can download the BSA FASTA file from here:
(also, I am attaching the bsa.fasta file. It only has one protein in it.)

Skyline has a peptide search engine called "MSAmanda". Here is the tutorial for that:

I hope this helps.
I do not know how to use a mass spectrometer, but if you tell us what data files you have, we might be able to give you advice about how you can analyze them.
-- Nick
MS-SZAOmics responded:  2022-11-29
Dear Nick,

You are very kind, thank you so much for your time and your information. As I said that, I'm very new in this area. Firstly, I started with BSA analysis. If I have any problems after completing some Skyline tutorials by doing BSA analysis, I will write it here again. Thanks a lot again for your help.