Link: http://db.systemsbiology.net:8080/proteomicsToolkit/FragIonServlet.html 5.

Question

Link:

http://db.systemsbiology.net:8080/proteomicsToolkit/FragIonServlet.html

5. You have isolated an important protein and by various biochemical assays have narrowed down the possible identity of the protein as one of the following three Protein A MQNSANHGRGFAMWEVPPRRKL RKGCPVWESTLDVVNSLSDRIRQACGCA Protein B MQLHQVFPRSISLARINVCPNPKTDRLSGNTIMMREPVWLTNSWKGLTLIR Protein C MLNLYPAGEVAPLPPQTAIPPSMRGVLHKPLVSWIRHPTRNEIAKSIEFMR (A) You fragment with a trypsin which we will assume cuts after every K. (Which is not 100% accurate but we will assume for this homework.) Build a table of all the masses of expected fragments from the three proteins above using the website: http://db.systemsbiolo net 8080/proteomics Toolkit/Fra onServlet.html to calculate the fragment sizes using the Mono (M+H) mass. The table should include the sequence of the fragment and it's Mono (M+H) mass.

Explanation / Answer

5. Three important proteins are isolated through biochemical assays and the following identifications are done-

A) Following are the fragments obtained after the trypsin digestion and their respective mono masses -

Protein A

MQNSANHGRGFAMWEVPPRRKLRK     (M+H)+ - 2868.35552

GCPVWESTLDVVNSLSDRIRQACGCA      (M+H)+ - 2781.14820

Protein B

MQLHQVFPRSISLARNVCPNPK             (M+H)+ - 2537. 08144

TDRLSGNTIMMREPVWLTNSWK                        (M+H)+ - 2637.04604

GLTLIR                                                          (M+H)+ - 672.84540

Protein C

MLNLYPAGEVAPLPPQTAIPPSMRGVLHK      (M+H)+ - 3099.72228

PLVSWRHPTRNEIAK                                (M+H)+ - 1805.09212

SIEFMR                                                         (M+H)+ - 782.93232

B) After running the three proteins through MALDI spectrum, it is observed that out protein of interest is PROTEIN C. Because, it showed the three fragments on the spectrum graph obtained after the trypsin digestion.

C) The fragment 1001.8 might have come from an unwanted digestion of proteins. It usually happens in the MALDI process. Hence, it does not affect the answer to the part B.

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