Protein sequencing

Limitations
Proteolysis does not always yield a set of
readily analyzable peptides covering the

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entire sequence of POI. The
fragmentation of peptides in the mass
spectrometer often does not yield ions
corresponding to cleavage at each
peptide bond. Thus, the deduced
sequence for each peptide is not
necessarily complete. The standard
methods of fragmentation do not
distinguish between leucine and
isoleucine residues since they are
isomeric.
Because the Edman degradation
proceeds from the N-terminus of the
protein, it will not work if the N-terminus
has been chemically modified (e.g. by
acetylation or formation of Pyroglutamic

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acid). Edman degradation is generally not
useful to determine the positions of
disulfide bridges. It also requires peptide
amounts of 1 picomole or above for
discernible results, making it less
sensitive than mass spectrometry.
In biology, proteins are produced by
translation of messenger RNA (mRNA)
with the protein sequence deriving from
the sequence of codons in the mRNA.
The mRNA is itself formed by the
transcription of genes and may be
further modified. These processes are
sufficiently understood to use computer
Predicting from DNA/RNA
sequences

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algorithms to automate predictions of
protein sequences from DNA sequences,
such as from whole-genome DNA-
sequencing projects, and have led to the
generation of large databases of protein
sequences such as UniProt. Predicted
protein sequences are an important
resource for protein identification by
mass spectrometry.
Historically, short protein sequences (10
to 15 residues) determined by Edman
degradation were back-translated into
DNA sequences that could be used as
probes or primers to isolate molecular
clones of the corresponding gene or
complementary DNA. The sequence of

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the cloned DNA was then determined
and used to deduce the full amino-acid
sequence of the protein.
Bioinformatics tools exist to assist with
interpretation of mass spectra (see de
novo peptide sequencing), to compare or
analyze protein sequences (see
sequence analysis), or search databases
using peptide or protein sequences (see
BLAST).
Bioinformatics tools

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The difficulty of protein sequencing was
recently proposed (https://eprint.iacr.org/
2022/658.pdf) as a basis for creating k-
time programs, programs that run exactly
k times before self-destructing. Such a
thing is impossible to build purely in
software because all software is
inherently clonable an unlimited number
of times.
Proteomics
DNA sequencing
Applications to
cryptography
See also

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Klaus Biemann
Donald F. Hunt
Matthias Mann
John R. Yates
1. Bogosian G, Violand BN, Dorward-King EJ,
Workman WE, Jung PE, Kane JF (January
1989). "Biosynthesis and incorporation
into protein of norleucine by Escherichia
coli" (https://doi.org/10.1016%2FS0021-9
258%2817%2931291-7) . The Journal of
Biological Chemistry. 264 (1): 531–9.
doi:10.1016/S0021-9258(17)31291-7 (htt
ps://doi.org/10.1016%2FS0021-9258%28
17%2931291-7) . PMID 2642478 (https://