Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass Spectrometry

Author(s):  
Nathan Edwards ◽  
Ross Lippert
2005 ◽  
Vol 71 (8) ◽  
pp. 4478-4486 ◽  
Author(s):  
Harry B. Hines ◽  
Frank Lebeda ◽  
Martha Hale ◽  
Ernst E. Brueggemann

ABSTRACT Botulinum toxin analysis has renewed importance. This study included the use of nanochromatography-nanoelectrospray-mass spectrometry/mass spectrometry to characterize the protein composition of botulinum progenitor toxins and to assign botulinum progenitor toxins to their proper serotype and strain by using currently available sequence information. Clostridium botulinum progenitor toxins from strains Hall, Okra, Stockholm, MDPH, Alaska, and Langeland and 89 representing serotypes A through G, respectively, were reduced, alkylated, digested with trypsin, and identified by matching the processed product ion spectra of the tryptic peptides to proteins in accessible databases. All proteins known to be present in progenitor toxins from each serotype were identified. Additional proteins, including flagellins, ORF-X1, and neurotoxin binding protein, not previously reported to be associated with progenitor toxins, were present also in samples from several serotypes. Protein identification was used to assign toxins to a serotype and strain. Serotype assignments were accurate, and strain assignments were best when either sufficient nucleotide or amino acid sequence data were available. Minor difficulties were encountered using neurotoxin-associated protein identification for assigning serotype and strain. This study found that combined nanoscale chromatographic and mass spectrometric techniques can characterize C. botulinum progenitor toxin protein composition and that serotype/strain assignments based upon these proteins can provide accurate serotype and, in most instances, strain assignments using currently available information. Assignment accuracy will continue to improve as more nucleotide/amino acid sequence information becomes available for different botulinum strains.


1979 ◽  
Vol 57 (6) ◽  
pp. 737-748 ◽  
Author(s):  
Theo Hofmann ◽  
Michiko Kawakami ◽  
Anthony J. W. Hitchman ◽  
Joan E. Harrison ◽  
Keith J. Dorrington

The complete amino acid sequence of the calcium-binding protein (CaBP) from pig intestinal mucosa has been determined: Ac-Ser-Ala-Gln-Lys-Ser-Pro-Ala-Glu-Leu-Lys-Ser-Ile-Phe-Glu-Lys-Tyr-Ala-Ala-Lys-Glu-Gly-Asp-Pro-Asn-Gln-Leu-Ser-Lys-Glu-Glu-Leu-Lys-Gln-Leu-Ile-Gln-Ala-Glu-Phe-Pro-Ser-Leu-Leu-Lys-Gly-Pro-Arg-Thr-Leu-Asp-Asp-Leu-Phe-Gln-Glu-Leu-Asp-Lys-Asn-Gly-Asn-Gly-Glu-Val-Ser-Phe-Glu-Glu-Phe-Gln-Val-Leu-Val-Lys-Lys-Ile-Ser-Gln-OH. The N-terminal octapeptide sequence was determined by mass spectrometry analysis by Morris and Dell. The first 45 residues of bovine CaBP differ only in six positions from the corresponding sequence of the porcine protein, except that the sequence starts in position two of the porcine sequence. The mammalian intestinal CaBP's belong to the troponin-C superfamily on the basis of an analysis by Barker and Dayhoff.


RSC Advances ◽  
2017 ◽  
Vol 7 (78) ◽  
pp. 49194-49203 ◽  
Author(s):  
Li-Tao Tong ◽  
Zhiyuan Ju ◽  
Ju Qiu ◽  
Lili Wang ◽  
Liya Liu ◽  
...  

The amino acid sequence of the peptide, GEQQQQPGM was determined by LC-mass spectrometry (MS)/MS.


Toxicon ◽  
2008 ◽  
Vol 51 (8) ◽  
pp. 1499-1508 ◽  
Author(s):  
Elisabeth F. Schwartz ◽  
Thalita S. Camargos ◽  
Fernando Z. Zamudio ◽  
Luciano P. Silva ◽  
Carlos Bloch ◽  
...  

1995 ◽  
Vol 217 (1) ◽  
pp. 257-263 ◽  
Author(s):  
D.M. Burgisser ◽  
G. Siegenthaler ◽  
T. Kuster ◽  
U. Hellman ◽  
P. Hunziker ◽  
...  

FEBS Letters ◽  
1970 ◽  
Vol 7 (1) ◽  
pp. 8-12 ◽  
Author(s):  
M.M. Shemyakin ◽  
Yu.A. Ovchinnikov ◽  
E.I. Vinogradova ◽  
A.A. Kiryushkin ◽  
M.Yu. Feigina ◽  
...  

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