I have a raw file of tandem mass spectrometry (LC-MS/MS) data. I want do online protein databank search for my protein identification and its homology.
Mr. Kamei,
The so-called ''fingerprinting approach'' does not provide neither reliable quantitative, nor qualitative information about such systems by mass spectrometry (MS.)
There is, currently, developed only our own-authored (my and my co-author's according to the authorship) stochastic dynamic method and model formulas which are capable of providing exact, not only qualitative, but also quantitative and even 3D structural information about the analytes mass spectrometrically. Please, consider in this context references [1-3].
[1] Stochastic Dynamic Mass Spectrometric Approach to Quantify Reserpine in Solution; Bojidarka Ivanova, Michael Spiteller
Analytical Chemistry Letters, 10 (2020) 703-721; Received 13 Oct 2020, Accepted 16 Dec 2020, Published online: 28 Jan 2021
Download citation https://doi.org/10.1080/22297928.2020.1865834
[2] Steroids, 164 (2020) 108750
Stochastic dynamic mass spectrometric quantification of steroids in mixture — Part II; Bojidarka Ivanova, Michael Spiteller
[3] Reviews in Analytical Chemistry, Band 38: Heft 2 (2019)
A stochastic dynamic mass spectrometric diffusion method and its application to 3D structural analysis of the analytes; Bojidarka Ivanova, Michael Spiteller
The mass spectrometric phenomena yielding to these set of experimental variables (or ''peaklist'' in your posting) such as m/z- and 'intensity'-values of the MS peaks obey a certain law. The model function cannot be derived only mathematically. Please, consider reference [4], as well. Therefore, the observable variables and the corresponding parameters according to the shown in the latter reference equation are mutually connected. In addition, the 'intenity'-value of a MS peak reflects exactly the free Gibbs energy parameter of a concrete and unique 3D molecular structure of the molecular/ionic species (see, more detail on reference [3], in this context.)
[4] Bioorganic Chemistry, 93 (2019) 103308
A mass spectrometric stochastic dynamic diffusion approach to selective quantitative and 3D structural analyses of native cyclodextrins by electrospray ionization and atmospheric pressure chemical ionization methods
Bojidarka Ivanova, Michael Spiteller
Obviously enough, there is unable only by means of statistical mathematical methods to gain reliable analytical chemical information by mass spectrometry.
The so-called ''identification'' in your posting of your analyte, has an exact analytical chemistry term. It is 'qualitative chemical analysis.'
Hello Rana,
Software to generate peaklist data for Mascot depends on the vendor of the mass spectrometer used to generate your raw data. Find your instrument vendor under "Instrument Specific Tips" on this website: http://www.matrixscience.com/help.html
There you will see available options to generate a peaklist file (usually .mgf) that can be loaded into Mascot. Note that many of the noted options use commercial software, so access could be limited.
Hope this helps,
Andrew
Open raw file in LC-MS software then export into excel or .text format.
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