Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation

Mikhail M Savitski, Frank Kjeldsen, Michael L Nielsen, Roman A Zubarev

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

Udgivelsesdato: 2007-Jul
OriginalsprogEngelsk
TidsskriftJournal of Proteome Research
Vol/bind6
Udgave nummer7
Sider (fra-til)2669-2673
Antal sider4
ISSN1535-3893
DOI
StatusUdgivet - 1. jul. 2007

Fingeraftryk

Ammonia
Ions
Amino Acids
Water
Isotopes
Databases
Oxygen
Peptides
Chemical activation

Citer dette

Savitski, Mikhail M ; Kjeldsen, Frank ; Nielsen, Michael L ; Zubarev, Roman A. / Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation. I: Journal of Proteome Research. 2007 ; Bind 6, Nr. 7. s. 2669-2673.
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title = "Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation",
abstract = "Analysis of a database containing over 20,000 high-resolution collision-activation mass spectra of tryptic peptide dications was employed to study the relative specificity of neutral losses from backbone fragments. The high resolution of the FTMS instrument allowed for the first time the first isotope of the water loss and the monoisotope of the ammonia loss to be distinguished. Contrary to a popular belief, water losses from y' ions are not specific enough to rely upon for detecting the presence of amino acids with oxygen in the side chains. At the same time, ammonia loss from b ions is sufficiently specific (>95{\%}) to detect the presence of amino acids Gln, Asn, His, Lys, and Arg. This feature will be useful for de novo algorithms for high-resolution MS data. Clear trends were observed when the effect of amino acids proximate to the cleavage site on the rate of loss formation was studied. These trends turned out to be different for losses from b and y ions.",
keywords = "Amino Acid Sequence, Amino Acids, Ammonia, Databases, Protein, Fourier Analysis, Mass Spectrometry, Molecular Sequence Data, Peptides, Sequence Analysis, Protein, Trypsin, Water",
author = "Savitski, {Mikhail M} and Frank Kjeldsen and Nielsen, {Michael L} and Zubarev, {Roman A}",
year = "2007",
month = "7",
day = "1",
doi = "10.1021/pr070121z",
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Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation. / Savitski, Mikhail M; Kjeldsen, Frank; Nielsen, Michael L; Zubarev, Roman A.

I: Journal of Proteome Research, Bind 6, Nr. 7, 01.07.2007, s. 2669-2673.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation

AU - Savitski, Mikhail M

AU - Kjeldsen, Frank

AU - Nielsen, Michael L

AU - Zubarev, Roman A

PY - 2007/7/1

Y1 - 2007/7/1

N2 - Analysis of a database containing over 20,000 high-resolution collision-activation mass spectra of tryptic peptide dications was employed to study the relative specificity of neutral losses from backbone fragments. The high resolution of the FTMS instrument allowed for the first time the first isotope of the water loss and the monoisotope of the ammonia loss to be distinguished. Contrary to a popular belief, water losses from y' ions are not specific enough to rely upon for detecting the presence of amino acids with oxygen in the side chains. At the same time, ammonia loss from b ions is sufficiently specific (>95%) to detect the presence of amino acids Gln, Asn, His, Lys, and Arg. This feature will be useful for de novo algorithms for high-resolution MS data. Clear trends were observed when the effect of amino acids proximate to the cleavage site on the rate of loss formation was studied. These trends turned out to be different for losses from b and y ions.

AB - Analysis of a database containing over 20,000 high-resolution collision-activation mass spectra of tryptic peptide dications was employed to study the relative specificity of neutral losses from backbone fragments. The high resolution of the FTMS instrument allowed for the first time the first isotope of the water loss and the monoisotope of the ammonia loss to be distinguished. Contrary to a popular belief, water losses from y' ions are not specific enough to rely upon for detecting the presence of amino acids with oxygen in the side chains. At the same time, ammonia loss from b ions is sufficiently specific (>95%) to detect the presence of amino acids Gln, Asn, His, Lys, and Arg. This feature will be useful for de novo algorithms for high-resolution MS data. Clear trends were observed when the effect of amino acids proximate to the cleavage site on the rate of loss formation was studied. These trends turned out to be different for losses from b and y ions.

KW - Amino Acid Sequence

KW - Amino Acids

KW - Ammonia

KW - Databases, Protein

KW - Fourier Analysis

KW - Mass Spectrometry

KW - Molecular Sequence Data

KW - Peptides

KW - Sequence Analysis, Protein

KW - Trypsin

KW - Water

U2 - 10.1021/pr070121z

DO - 10.1021/pr070121z

M3 - Journal article

C2 - 17503798

VL - 6

SP - 2669

EP - 2673

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 7

ER -