scholarly journals Study by mass spectrometry of amino acid sequences in peptides containing histidine

1970 ◽  
Vol 117 (2) ◽  
pp. 31P-32P ◽  
Author(s):  
J F G Vliegenthart ◽  
L Dorland
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Amino Acid Sequences

Resolution of a protein sequence ambiguity by X-ray crystallographic and mass spectrometric methods

1992 ◽  
Vol 25 (2) ◽  
pp. 205-210 ◽  
Author(s):  
L. J. Keefe ◽  
E. E. Lattman ◽  
C. Wolkow ◽  
A. Woods ◽  
M. Chevrier ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Electron Density ◽  
Mass Spectrometric ◽  
Amino Acid Sequences ◽  
Data Matrix ◽  
Protein Crystal ◽  
Insertion Mutant ◽  
Laser Desorption Mass Spectrometry ◽  
X Ray

Ambiguities in amino acid sequences are a potential problem in X-ray crystallographic studies of proteins. Amino acid side chains often cannot be reliably identified from the electron density. Many protein crystal structures that are now being solved are simple variants of a known wild-type structure. Thus, cloning artifacts or other untoward events can readily lead to cases in which the proposed sequence is not correct. An example is presented showing that mass spectrometry provides an excellent tool for analyzing suspected errors. The X-ray crystal structure of an insertion mutant of Staphylococcal nuclease has been solved to 1.67 Å resolution and refined to a crystallographic R value of 0.170 [Keefe & Lattman (1992). In preparation]. A single residue has been inserted in the C-terminal α helix. The inserted amino acid was believed to be an alanine residue, but the final electron density maps strongly indicated that a glycine had been inserted instead. To confirm the observations from the X-ray data, matrix-assisted laser desorption mass spectrometry was employed to verify the glycine insertion. This mass spectrometric technique has sufficient mass accuracy to detect the methyl group that distinguishes glycine from alanine and can be extended to the more common situation in which crystallographic measurements suggest a problem with the sequence, but cannot pinpoint its location or nature.

New Antibiotic Uperin Peptides From the Dorsal Glands of the Australian Toadlet Uperoleia mjobergii

1996 ◽  
Vol 49 (12) ◽  
pp. 1325 ◽  
Author(s):  
AM Bradford ◽  
JH Bowie ◽  
MJ Tyler ◽  
JC Wallace
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Related Species ◽  
Antibiotic Activity ◽  
Amino Acid Sequences ◽  
The Other ◽  
Cationic Peptides ◽  
Amino Acid Residues ◽  
Skin Glands ◽  
Edman Sequencing

The dorsal glandular extract of the toadlet Uperoleia mjobergii contains more than 20 peptides. We report the amino acid sequences of the seven major peptides: these were determined by a combination of mass spectrometry and automated Edman sequencing. Three of these peptides have 19 amino acid residues and belong to the uperin 2 group of peptides [e.g. uperin 2.6, Gly Ile Leu Asp Ile Ala Lys Lys Leu Val Gly Gly Ile Arg Asn Val Leu Gly Ile (OH)], while the other four have 17 residues and are classified as uperins 3 [e.g. Uperin 3.4, Gly Val Gly Asp Leu Ile Arg Lys Ala Val Ala Ala Ile Lys Asn Ile Val (NH2)]. Several of these cationic peptides have been synthesized in order for bioassays to be carried out: they show significant antibiotic activity against a range of Gram-positive microorganisms. A major skin peptide from the related species Uperoleia inundata is a powerful neuropeptide named uperin 1.1 ([Ala2] uperolein ): no corresponding neuropeptide is detected in the skin glands of Uperoleia mjobergii.

Mass spectrometric studies of peptides. V. Determination of amino acid sequences in peptide mixtures by mass spectrometry

1973 ◽  
Vol 95 (10) ◽  
pp. 3369-3375 ◽  
Author(s):  
Hans Kaspar. Wipf ◽  
Philip. Irving ◽  
Malcolm. McCamish ◽  
Rengachari. Venkataraghavan ◽  
F. W. McLafferty
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Mass Spectrometric ◽  
Amino Acid Sequences ◽  
Peptide Mixtures

scholarly journals Determination of amino acid sequences in peptides by mass spectrometry. Desulfurization of sulfur-containing peptides

FEBS Letters ◽  
1970 ◽  
Vol 8 (4) ◽  
pp. 207-209 ◽  
Author(s):  
R. Toubiana ◽  
J.E.G. Barnett ◽  
E. Sach ◽  
B.C. Das ◽  
E. Lederer
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Amino Acid Sequences ◽  
Sulfur Containing

Determination of amino acid sequences in oligopeptides by mass spectrometry. II. The structure of peptidolipin NA

1965 ◽  
Vol 6 (18) ◽  
pp. 1331-1336 ◽  
Author(s):  
M. Barber ◽  
W.A. Wolstenholme ◽  
M. Guinand ◽  
G. Michel ◽  
B.C. Das ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Amino Acid Sequences

scholarly journals Spritz: A Proteogenomic Database Engine

2020 ◽  
Author(s):  
Anthony J. Cesnik ◽  
Rachel M. Miller ◽  
Khairina Ibrahim ◽  
Lei Lu ◽  
Robert J. Millikin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Cell Line ◽  
Rna Sequencing ◽  
Amino Acid Sequences ◽  
Osteosarcoma Cell ◽  
Sequencing Data ◽  
Protein Database ◽  
Bottom Up ◽  
Sequence Variations

AbstractProteoforms are the workhorses of the cell, and subtle differences between their amino acid sequence or post-translational modifications (PTMs) can change their biological function. To most effectively identify and quantify proteoforms in genetically diverse samples by mass spectrometry (MS), it is advantageous to search the MS data against a sample-specific protein database that is tailored to the sample being analyzed, in that it contains the correct amino acid sequences and relevant PTMs for that sample. To this end, we have developed Spritz (https://smith-chem-wisc.github.io/Spritz/), an open-source software tool for generating protein databases annotated with sequence variations and PTMs. We provide a simple graphical user interface (GUI) for Windows and scripts that can be run on any operating system. Spritz automatically sets up and executes approximately 20 tools, which enable construction of a proteogenomic database from only raw RNA sequencing data. Sequence variations that are discovered in RNA sequencing data upon comparison to the Ensembl reference genome are annotated on proteins in these databases, and PTM annotations are transferred from UniProt. Modifications can also be discovered and added to the database using bottom-up mass spectrometry data and global PTM discovery in MetaMorpheus. We demonstrate that such sample-specific databases allow the identification of variant peptides, modified variant peptides, and variant proteoforms by searching bottom-up and top-down proteomic data from the Jurkat human T lymphocyte cell line and demonstrate the identification of phosphorylated variant sites with phosphoproteomic data from the U2OS human osteosarcoma cell line.

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