Chromatography Forum

I sent my samples (EP and GP) for LC-MS analysis and got the protein identity. When I looked at the spectrum for labeling, there were two spectrums for each sample in different colours. Why are there 2 spectrums and what do they stand for/mean? How do I know which peak is my sample? I wish I could upload the image here but I don't know how. Confused. Please help. Thank you

There are a couple of possibilities. The most likely is that you have the positive and negative ion spectra from each compound (look to see if there is a pos/neg annotaion anywhere). Another possibility is that they come from different ionisation modes, several manufacturers instruments are capable of alternating the ionisation modes, to get for example electrospray and atmospheric pressure chemical ionisation spectra (look for ES and AP annotations).

Or, if this an analysis you actually paid for, let the service provider explain the spectra to you.

For the GP, one had TOF MS ES+ 2.19E3 while the other had TOF MS ES+ 2.40e3. EP had TOF MS ES+ 684 and TOF MS ES+ 948. I was told there were two specra because samples were injected twice (like replicates) and only through software and computer we can identify which ionization peak represents the sample. Is this correct?

The codes you've posted tell us that:
-the machine used is a time-of-flight (TOF)
-ionization mode was positive electrospray in alal cases (ES+)
-the strongest signal are 2193 and 948 ion counts respectively (2.40e3 and 948)

So now we know that you have two replicates of each samples, all generated with the same procedure. One sample gave a much stronger signal and the other weaker. But this is clearly not enough for interpretation. In which format did you get the spectra? And what are you interested in? If you sent proteins to a lab for analysis I guess you wanted to get some information from them, could please explain better?