7 research outputs found
Parallel Proteomic Workflow for Mass Spectrometric Analysis of Tissue Samples Preserved by Different Methods
Formalin-fixed
and paraffin-embedded (FFPE) and optimal cutting
temperature (OCT)-embedded and frozen tissue specimens in biobanks
are highly valuable in clinical studies but proteomic and post-translational
modification (PTM) studies using mass spectrometry (MS) have been
limited due to structural arrangement of proteins and contaminations
from embedding material. This study aims to develop a parallel proteomic
workflow for FFPE and OCT/frozen samples that allows for large-scale,
quick, reproducible, qualitative, and quantitative high-resolution
MS analysis. The optimized protocol gives details on removal of embedding
material, protein extraction, and multienzyme digestion using filter-aided
sample preparation method. The method was evaluated by investigating
the protein expression levels in nonmuscle-invasive and muscle-invasive
bladder cancer samples in two cohorts and MS spectra were carefully
reviewed for contaminations. More than 2000 and 3000 proteins in FFPE
and OCT/frozen samples, respectively, were identified, and samples
could be clustered in different tumor stages based on their protein
expression. Furthermore, more than 250 and 400 phosphopeptides could
be identified from specific patient samples of FFPE and OCT/frozen,
respectively, using titanium dioxide enrichment. The paper presents
unique data describing the similarities and differences observed in
FFPE and OCT/frozen samples and shows the feasibility to detect proteins
and site-specific phosphorylation even after long-term storage of
clinical samples
Parallel Proteomic Workflow for Mass Spectrometric Analysis of Tissue Samples Preserved by Different Methods
Formalin-fixed
and paraffin-embedded (FFPE) and optimal cutting
temperature (OCT)-embedded and frozen tissue specimens in biobanks
are highly valuable in clinical studies but proteomic and post-translational
modification (PTM) studies using mass spectrometry (MS) have been
limited due to structural arrangement of proteins and contaminations
from embedding material. This study aims to develop a parallel proteomic
workflow for FFPE and OCT/frozen samples that allows for large-scale,
quick, reproducible, qualitative, and quantitative high-resolution
MS analysis. The optimized protocol gives details on removal of embedding
material, protein extraction, and multienzyme digestion using filter-aided
sample preparation method. The method was evaluated by investigating
the protein expression levels in nonmuscle-invasive and muscle-invasive
bladder cancer samples in two cohorts and MS spectra were carefully
reviewed for contaminations. More than 2000 and 3000 proteins in FFPE
and OCT/frozen samples, respectively, were identified, and samples
could be clustered in different tumor stages based on their protein
expression. Furthermore, more than 250 and 400 phosphopeptides could
be identified from specific patient samples of FFPE and OCT/frozen,
respectively, using titanium dioxide enrichment. The paper presents
unique data describing the similarities and differences observed in
FFPE and OCT/frozen samples and shows the feasibility to detect proteins
and site-specific phosphorylation even after long-term storage of
clinical samples
Comprehensive Proteomic Study of the Antiproliferative Activity of a Polyphenol-Enriched Rosemary Extract on Colon Cancer Cells Using Nanoliquid Chromatography–Orbitrap MS/MS
In this work, a proteomics strategy
based on nanoliquid chromatography–tandem
mass spectrometry (nano-LC–MS/MS) using an Orbitrap high-resolution
mass spectrometer together with stable isotope dimethyl labeling (DML)
is applied to quantitatively examine relative changes in the protein
fraction of HT-29 human colon cancer cells treated with different
concentrations of a polyphenol-enriched rosemary extract over the
time. The major objective of this study was to gain insights into
the antiproliferative mechanisms induced by rosemary polyphenols.
Using this methodology, 1909 and 698 proteins were identified and
quantified in cell extracts. The polyphenol-enriched rosemary extract
treatment changed the expression of several proteins in a time- and
concentration-dependent manner. Most of the altered proteins are implicated
in the activation of Nrf2 transcription factor and the unfolded protein
response. In conclusion, rosemary polyphenols induced proteomic changes
that were related to the attenuation of aggresome formation and activation
of autophagy to alleviate cellular stress
Comprehensive Proteomic Study of the Antiproliferative Activity of a Polyphenol-Enriched Rosemary Extract on Colon Cancer Cells Using Nanoliquid Chromatography–Orbitrap MS/MS
In this work, a proteomics strategy
based on nanoliquid chromatography–tandem
mass spectrometry (nano-LC–MS/MS) using an Orbitrap high-resolution
mass spectrometer together with stable isotope dimethyl labeling (DML)
is applied to quantitatively examine relative changes in the protein
fraction of HT-29 human colon cancer cells treated with different
concentrations of a polyphenol-enriched rosemary extract over the
time. The major objective of this study was to gain insights into
the antiproliferative mechanisms induced by rosemary polyphenols.
Using this methodology, 1909 and 698 proteins were identified and
quantified in cell extracts. The polyphenol-enriched rosemary extract
treatment changed the expression of several proteins in a time- and
concentration-dependent manner. Most of the altered proteins are implicated
in the activation of Nrf2 transcription factor and the unfolded protein
response. In conclusion, rosemary polyphenols induced proteomic changes
that were related to the attenuation of aggresome formation and activation
of autophagy to alleviate cellular stress
Parallel Proteomic Workflow for Mass Spectrometric Analysis of Tissue Samples Preserved by Different Methods
Formalin-fixed
and paraffin-embedded (FFPE) and optimal cutting
temperature (OCT)-embedded and frozen tissue specimens in biobanks
are highly valuable in clinical studies but proteomic and post-translational
modification (PTM) studies using mass spectrometry (MS) have been
limited due to structural arrangement of proteins and contaminations
from embedding material. This study aims to develop a parallel proteomic
workflow for FFPE and OCT/frozen samples that allows for large-scale,
quick, reproducible, qualitative, and quantitative high-resolution
MS analysis. The optimized protocol gives details on removal of embedding
material, protein extraction, and multienzyme digestion using filter-aided
sample preparation method. The method was evaluated by investigating
the protein expression levels in nonmuscle-invasive and muscle-invasive
bladder cancer samples in two cohorts and MS spectra were carefully
reviewed for contaminations. More than 2000 and 3000 proteins in FFPE
and OCT/frozen samples, respectively, were identified, and samples
could be clustered in different tumor stages based on their protein
expression. Furthermore, more than 250 and 400 phosphopeptides could
be identified from specific patient samples of FFPE and OCT/frozen,
respectively, using titanium dioxide enrichment. The paper presents
unique data describing the similarities and differences observed in
FFPE and OCT/frozen samples and shows the feasibility to detect proteins
and site-specific phosphorylation even after long-term storage of
clinical samples
Parallel Proteomic Workflow for Mass Spectrometric Analysis of Tissue Samples Preserved by Different Methods
Formalin-fixed
and paraffin-embedded (FFPE) and optimal cutting
temperature (OCT)-embedded and frozen tissue specimens in biobanks
are highly valuable in clinical studies but proteomic and post-translational
modification (PTM) studies using mass spectrometry (MS) have been
limited due to structural arrangement of proteins and contaminations
from embedding material. This study aims to develop a parallel proteomic
workflow for FFPE and OCT/frozen samples that allows for large-scale,
quick, reproducible, qualitative, and quantitative high-resolution
MS analysis. The optimized protocol gives details on removal of embedding
material, protein extraction, and multienzyme digestion using filter-aided
sample preparation method. The method was evaluated by investigating
the protein expression levels in nonmuscle-invasive and muscle-invasive
bladder cancer samples in two cohorts and MS spectra were carefully
reviewed for contaminations. More than 2000 and 3000 proteins in FFPE
and OCT/frozen samples, respectively, were identified, and samples
could be clustered in different tumor stages based on their protein
expression. Furthermore, more than 250 and 400 phosphopeptides could
be identified from specific patient samples of FFPE and OCT/frozen,
respectively, using titanium dioxide enrichment. The paper presents
unique data describing the similarities and differences observed in
FFPE and OCT/frozen samples and shows the feasibility to detect proteins
and site-specific phosphorylation even after long-term storage of
clinical samples
Conocimiento y lenguaje. Problemas de semántica
Ponència del professor Helmut Gipper, de Münster, en el marc del seminari dedicat a les qüestions i punts de vista filosòfics d'Adam Schaf