I have three native plant proteins. After digesting them, their peptides were analyzed through LCMS Agilant MassHunter qualitative analysis. I have no idea how to analyze the chromatogram peaks and spectra peaks through TIC Scan, ESI Scan, and all. Please, someone guide me on how I could interpret it and identify the proteins, as I have raw data.
To better understand what you are asking, please first familiar yourself with the basics of HPLC and also HPLC-MS (LC-MS) analysis. Interpretation of the data requires that you first understand the techniques used and instrument settings. Their are no "universal settings" so errors are easy to make. Please contact a professional LC-MS laboratory or experienced industrial chromatographer at your school for assistance. Without initial training, no one can provide instruction in "how to perform LC-MS" interpretation via a 'web forum' or a class. Using an LC-MS system is not the same as learning how to use a spectrophotometer or other basic tool. Learning just the basics of this complex technique just for one group of compounds and/or one mode of chromatography can take many years of full-time work.
As a student, your time may be best spent learning how to work with someone who already has this experience and can help you directly with your project. This will increase the chances that the data YOU collect and any interpretations made are accurate.
- *An LC-MS system will always output data, but only when setup by a skilled operator with many years of professional training with a valid HPLC method and proper settings will the data be of use to you. Never assume that the data you have collected is valid until after the method has been evaluated by a professional chromatographer. Correct interpretation can not start until after the method used has been checked (NOTE: Many LC-MS methods that we review turn out to be invalid so any conclusions drawn are also invalid).
The above process will also save you the most time and teach you an important skill (**how to work with other scientists who have the years of experience in areas outside of your own).
Now you must collect some previous research data or database by which the data can be matched. also if standard were used math the peaks run time/ RT values to get idea of any known compounds present in it or not.
lcms has two spectral data,
one in which the peak data with rt valus and peak hight are given and in another are m/z for each and every peak. you have to analyze the m/z data which have fragments of compounds present in the sample. more the peaks in peak data ,more will be pages in the lcms report having same number of compounds or impurities. then you can use any database with previously published articles or wellstablished databases to confirm the quantity (peak hight ) and exact mass (m/z). more can be discussed in private messages. hopefully you have now a proper idea for proceeding .
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