2004
DOI: 10.1002/rcm.1657
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Diagnostic protein discovery using proteolytic peptide targeting and identification

Abstract: Plasma protein profiling with mass spectrometry is currently being evaluated as a diagnostic tool for cancer and other diseases. These experiments consist of three steps: plasma protein fractionation, analysis with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS), and comparisons of the MALDI profiles to develop diagnostic fingerprints using bioinformatic techniques. While preliminary results appear promising in small sample groups, the method is limited by the sensiti… Show more

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Cited by 28 publications
(39 citation statements)
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“…Methods under development involve extraction/fractionation before tryptic digestion and high-resolution MALDI profiling of the peptides produced (48 ), as well as profiling of existing peptides with high-resolution MALDI after prefractionation based on reversed-phase magnetic particles and with subsequent data modeling (32 ). The latter study rigorously examined the circumstances necessary for generation of reproducible and complex spectra, including laser conditions and matrix composition.…”
Section: Discussionmentioning
confidence: 99%
“…Methods under development involve extraction/fractionation before tryptic digestion and high-resolution MALDI profiling of the peptides produced (48 ), as well as profiling of existing peptides with high-resolution MALDI after prefractionation based on reversed-phase magnetic particles and with subsequent data modeling (32 ). The latter study rigorously examined the circumstances necessary for generation of reproducible and complex spectra, including laser conditions and matrix composition.…”
Section: Discussionmentioning
confidence: 99%
“…In addition, other proteins with masses similar to that of biomarker proteins may give ion signals that overlap with each other on MALDI-TOF mass spectra. An alternative method for improving the characterization efficiency of low abundant or large intact proteins is through proteolytic digestion of the sample [304][305][306][307][308][309][310][311][312][313][314][315][316][317][318][319]. After digestion, the protein fragments detected by MALDI-TOF/MS in reflective mode within the lower mass range can be used to provide a characteristic high-resolution peptide profile.…”
Section: Rapid Digestionmentioning
confidence: 99%
“…After digestion, the protein fragments detected by MALDI-TOF/MS in reflective mode within the lower mass range can be used to provide a characteristic high-resolution peptide profile. If necessary, specific ions can be chosen for further MS/MS analysis for peptide sequencing [304][305][306][307][308][309][310][311][312][313][314][315][316][317][318][319]. Compared to intact protein profiling, the obtaining of highly resolved ion signals of representative peptides provide more sensitive and accurate diagnosis of proteins and extend the accessible protein molecular weight range.…”
Section: Rapid Digestionmentioning
confidence: 99%
“…There are numerous methods that are based on isotopically labeled protein modifying reagents to label or tag proteins to determine relative or absolute concentrations in complex mixtures. The higher resolution offered by the tandem Qq-TOF mass spectrometer is ideally suited to isotopically labeled applications (Gu et al, 2004;Koomen et al 2004;Ward et al, 1990). Applied Biosystems recently introduced iTRAQ reagents (Gu et al, 2004;Koomen et al 2004;Ward et al, 1990), which are amino reactive compounds that are used to label peptides in a total protein digest of a fluid such as saliva.…”
Section: Lc-ms/ms Mass Spectroscopy With Isotopic Labelingmentioning
confidence: 99%
“…The higher resolution offered by the tandem Qq-TOF mass spectrometer is ideally suited to isotopically labeled applications (Gu et al, 2004;Koomen et al 2004;Ward et al, 1990). Applied Biosystems recently introduced iTRAQ reagents (Gu et al, 2004;Koomen et al 2004;Ward et al, 1990), which are amino reactive compounds that are used to label peptides in a total protein digest of a fluid such as saliva. The real advantage is that the tag remains intact through TOF-MS analysis; however, it is revealed during collision induced dissociation by MSMS analysis.…”
Section: Lc-ms/ms Mass Spectroscopy With Isotopic Labelingmentioning
confidence: 99%