15 research outputs found
Assessment and Improvement of Statistical Tools for Comparative Proteomics Analysis of Sparse Data Sets with Few Experimental Replicates
Large-scale
quantitative analyses of biological systems are often
performed with few replicate experiments, leading to multiple nonidentical
data sets due to missing values. For example, mass spectrometry driven
proteomics experiments are frequently performed with few biological
or technical replicates due to sample-scarcity or due to duty-cycle
or sensitivity constraints, or limited capacity of the available instrumentation,
leading to incomplete results where detection of significant feature
changes becomes a challenge. This problem is further exacerbated for
the detection of significant changes on the peptide level, for example,
in phospho-proteomics experiments. In order to assess the extent of
this problem and the implications for large-scale proteome analysis,
we investigated and optimized the performance of three statistical
approaches by using simulated and experimental data sets with varying
numbers of missing values. We applied three tools, including standard <i>t</i> test, moderated <i>t</i> test, also known as
limma, and rank products for the detection of significantly changing
features in simulated and experimental proteomics data sets with missing
values. The rank product method was improved to work with data sets
containing missing values. Extensive analysis of simulated and experimental
data sets revealed that the performance of the statistical analysis
tools depended on simple properties of the data sets. High-confidence
results were obtained by using the limma and rank products methods
for analyses of triplicate data sets that exhibited more than 1000
features and more than 50% missing values. The maximum number of differentially
represented features was identified by using limma and rank products
methods in a complementary manner. We therefore recommend combined
usage of these methods as a novel and optimal way to detect significantly
changing features in these data sets. This approach is suitable for
large quantitative data sets from stable isotope labeling and mass
spectrometry experiments and should be applicable to large data sets
of any type. An R script that implements the improved rank products
algorithm and the combined analysis is available
Assessment and Improvement of Statistical Tools for Comparative Proteomics Analysis of Sparse Data Sets with Few Experimental Replicates
Large-scale
quantitative analyses of biological systems are often
performed with few replicate experiments, leading to multiple nonidentical
data sets due to missing values. For example, mass spectrometry driven
proteomics experiments are frequently performed with few biological
or technical replicates due to sample-scarcity or due to duty-cycle
or sensitivity constraints, or limited capacity of the available instrumentation,
leading to incomplete results where detection of significant feature
changes becomes a challenge. This problem is further exacerbated for
the detection of significant changes on the peptide level, for example,
in phospho-proteomics experiments. In order to assess the extent of
this problem and the implications for large-scale proteome analysis,
we investigated and optimized the performance of three statistical
approaches by using simulated and experimental data sets with varying
numbers of missing values. We applied three tools, including standard <i>t</i> test, moderated <i>t</i> test, also known as
limma, and rank products for the detection of significantly changing
features in simulated and experimental proteomics data sets with missing
values. The rank product method was improved to work with data sets
containing missing values. Extensive analysis of simulated and experimental
data sets revealed that the performance of the statistical analysis
tools depended on simple properties of the data sets. High-confidence
results were obtained by using the limma and rank products methods
for analyses of triplicate data sets that exhibited more than 1000
features and more than 50% missing values. The maximum number of differentially
represented features was identified by using limma and rank products
methods in a complementary manner. We therefore recommend combined
usage of these methods as a novel and optimal way to detect significantly
changing features in these data sets. This approach is suitable for
large quantitative data sets from stable isotope labeling and mass
spectrometry experiments and should be applicable to large data sets
of any type. An R script that implements the improved rank products
algorithm and the combined analysis is available
Spatial and Temporal Effects in Protein Post-translational Modification Distributions in the Developing Mouse Brain
Protein post-translational modification
(PTM) is a powerful way
to modify the behavior of cellular proteins and thereby cellular behavior.
Multiple recent studies of evolutionary trends have shown that certain
pairs of protein post-translational modifications tend to occur closer
to each other than expected at random. This type of observation may
form the basis of a proposed “PTM code”, whereby protein
function is controlled by complex patterns of multiple PTMs. This
code could provide an additional, powerful level of regulatory control
for protein function and is a plausible explanation for observations
of increasingly frequent and diverse protein modification in cell
biology. In this study, we use mass spectrometry and proteomic strategies
to present biological data showing spatiotemporal PTM co-localization
across multiple PTM categories, which display changes over development
of the brain. This may be an indication of the existence of a PTM-based
functional coding mechanism, which would significantly expand our
view of the ways in which cells use protein PTMs in complex signaling
networks
Spatial and Temporal Effects in Protein Post-translational Modification Distributions in the Developing Mouse Brain
Protein post-translational modification
(PTM) is a powerful way
to modify the behavior of cellular proteins and thereby cellular behavior.
Multiple recent studies of evolutionary trends have shown that certain
pairs of protein post-translational modifications tend to occur closer
to each other than expected at random. This type of observation may
form the basis of a proposed “PTM code”, whereby protein
function is controlled by complex patterns of multiple PTMs. This
code could provide an additional, powerful level of regulatory control
for protein function and is a plausible explanation for observations
of increasingly frequent and diverse protein modification in cell
biology. In this study, we use mass spectrometry and proteomic strategies
to present biological data showing spatiotemporal PTM co-localization
across multiple PTM categories, which display changes over development
of the brain. This may be an indication of the existence of a PTM-based
functional coding mechanism, which would significantly expand our
view of the ways in which cells use protein PTMs in complex signaling
networks
Performance of Isobaric and Isotopic Labeling in Quantitative Plant Proteomics
Mass spectrometry has become indispensable for peptide
and protein
quantification in proteomics studies. When proteomics technologies
are applied to understand the biology of plants, two-dimensional gel
electrophoresis is still the prevalent method for protein fractionation,
identification, and quantitation. In the present work, we have used
LC–MS to compare an isotopic (ICPL) and isobaric (iTRAQ) chemical
labeling technique to quantify proteins in the endosperm of <i>Ricinus communis</i> seeds at
three developmental stages (IV, VI, and X). Endosperm proteins of
each stage were trypsin-digested in-solution, and the same amount
of peptides was labeled with ICPL and iTRAQ tags in two orders (forward
and reverse). Each sample was submitted to nanoLC coupled to an LTQ-Orbitrap
high-resolution mass spectrometer. Comparing labeling performance,
iTRAQ was able to label 99.8% of all identified unique peptides, while
94.1% were labeled by ICPL. After statistical analysis, it was possible
to quantify 309 (ICPL) and 321 (iTRAQ) proteins, from which 95 are
specific to ICPL, 107 to iTRAQ, and 214 common to both labeling strategies.
We noted that the iTRAQ quantification could be influenced by the
tag. Even though the efficiency of the iTRAQ and ICPL in protein quantification
depends on several parameters, both labeling methods were able to
successfully quantify proteins present in the endosperm of castor
bean during seed development and, when combined, increase the number
of quantified proteins
Performance of Isobaric and Isotopic Labeling in Quantitative Plant Proteomics
Mass spectrometry has become indispensable for peptide
and protein
quantification in proteomics studies. When proteomics technologies
are applied to understand the biology of plants, two-dimensional gel
electrophoresis is still the prevalent method for protein fractionation,
identification, and quantitation. In the present work, we have used
LC–MS to compare an isotopic (ICPL) and isobaric (iTRAQ) chemical
labeling technique to quantify proteins in the endosperm of <i>Ricinus communis</i> seeds at
three developmental stages (IV, VI, and X). Endosperm proteins of
each stage were trypsin-digested in-solution, and the same amount
of peptides was labeled with ICPL and iTRAQ tags in two orders (forward
and reverse). Each sample was submitted to nanoLC coupled to an LTQ-Orbitrap
high-resolution mass spectrometer. Comparing labeling performance,
iTRAQ was able to label 99.8% of all identified unique peptides, while
94.1% were labeled by ICPL. After statistical analysis, it was possible
to quantify 309 (ICPL) and 321 (iTRAQ) proteins, from which 95 are
specific to ICPL, 107 to iTRAQ, and 214 common to both labeling strategies.
We noted that the iTRAQ quantification could be influenced by the
tag. Even though the efficiency of the iTRAQ and ICPL in protein quantification
depends on several parameters, both labeling methods were able to
successfully quantify proteins present in the endosperm of castor
bean during seed development and, when combined, increase the number
of quantified proteins
Performance of Isobaric and Isotopic Labeling in Quantitative Plant Proteomics
Mass spectrometry has become indispensable for peptide
and protein
quantification in proteomics studies. When proteomics technologies
are applied to understand the biology of plants, two-dimensional gel
electrophoresis is still the prevalent method for protein fractionation,
identification, and quantitation. In the present work, we have used
LC–MS to compare an isotopic (ICPL) and isobaric (iTRAQ) chemical
labeling technique to quantify proteins in the endosperm of <i>Ricinus communis</i> seeds at
three developmental stages (IV, VI, and X). Endosperm proteins of
each stage were trypsin-digested in-solution, and the same amount
of peptides was labeled with ICPL and iTRAQ tags in two orders (forward
and reverse). Each sample was submitted to nanoLC coupled to an LTQ-Orbitrap
high-resolution mass spectrometer. Comparing labeling performance,
iTRAQ was able to label 99.8% of all identified unique peptides, while
94.1% were labeled by ICPL. After statistical analysis, it was possible
to quantify 309 (ICPL) and 321 (iTRAQ) proteins, from which 95 are
specific to ICPL, 107 to iTRAQ, and 214 common to both labeling strategies.
We noted that the iTRAQ quantification could be influenced by the
tag. Even though the efficiency of the iTRAQ and ICPL in protein quantification
depends on several parameters, both labeling methods were able to
successfully quantify proteins present in the endosperm of castor
bean during seed development and, when combined, increase the number
of quantified proteins
Performance of Isobaric and Isotopic Labeling in Quantitative Plant Proteomics
Mass spectrometry has become indispensable for peptide
and protein
quantification in proteomics studies. When proteomics technologies
are applied to understand the biology of plants, two-dimensional gel
electrophoresis is still the prevalent method for protein fractionation,
identification, and quantitation. In the present work, we have used
LC–MS to compare an isotopic (ICPL) and isobaric (iTRAQ) chemical
labeling technique to quantify proteins in the endosperm of <i>Ricinus communis</i> seeds at
three developmental stages (IV, VI, and X). Endosperm proteins of
each stage were trypsin-digested in-solution, and the same amount
of peptides was labeled with ICPL and iTRAQ tags in two orders (forward
and reverse). Each sample was submitted to nanoLC coupled to an LTQ-Orbitrap
high-resolution mass spectrometer. Comparing labeling performance,
iTRAQ was able to label 99.8% of all identified unique peptides, while
94.1% were labeled by ICPL. After statistical analysis, it was possible
to quantify 309 (ICPL) and 321 (iTRAQ) proteins, from which 95 are
specific to ICPL, 107 to iTRAQ, and 214 common to both labeling strategies.
We noted that the iTRAQ quantification could be influenced by the
tag. Even though the efficiency of the iTRAQ and ICPL in protein quantification
depends on several parameters, both labeling methods were able to
successfully quantify proteins present in the endosperm of castor
bean during seed development and, when combined, increase the number
of quantified proteins
Precision Mapping of Coexisting Modifications in Histone H3 Tails from Embryonic Stem Cells by ETD-MS/MS
Post-translational
modifications (PTMs) of histones play a major
role in regulating chromatin dynamics and influence processes such
as transcription and DNA replication. Here, we report 114 distinct
combinations of coexisting PTMs of histone H3 obtained from mouse
embryonic stem (ES) cells. Histone H3 N-terminal tail peptides (amino
acids 1–50, 5–6 kDa) were separated by optimized weak
cation exchange/hydrophilic interaction liquid chromatography (WCX/HILIC)
and sequenced online by electron transfer dissociation (ETD) tandem
mass spectrometry (MS/MS). High mass accuracy and near complete sequence
coverage allowed unambiguous mapping of the major histone marks and
discrimination between isobaric and nearly isobaric PTMs such as trimethylation
and acetylation. Hierarchical data analysis identified H3K27me2-H3K36me2
as the most frequently observed PTMs in H3. Modifications at H3 residues
K27 and K36 often coexist with the abundant mark K23ac, and we identified
two frequently occurring quadruplet marks ‘K9me1K23acK27me2K36me2’
and ‘K9me3K23acK27me2K36me’, which might indicate a
role in crosstalk. Co-occurrence frequency analysis revealed also
an interplay between methylations of K9, K27, and K36, suggesting
interdependence between histone methylation marks. We hypothesize
that the most abundant coexisting PTMs may provide a signature for
the permissive state of mouse ES cells
Взаємозв'язок між якістю корпоративного управління та вартості банку в концентрованій системі власності: теоретичні основи
This article presents the results of evidence of corporate governance variable endogeneity and proposes different instruments for estimation by instrumental variables approach. Moreover, results by simultaneous equation approach indicate a relation of reverse causality between corporate governance quality and bank valuation. The empirical methodology developed in this article may be further used in the research; the study of relationship between corporate governance quality and bank value under the optimal ratio of ownership concentration is another promising area of study.У даній статті представлені результати докази корпоративного управління змінної ендогенного і пропонує різні інструменти для оцінки за допомогою інструментальних змінних підходу. Крім того, результати шляхом одночасного рівняння підходу вказують на ставлення зворотного причинно-наслідкового зв'язку між якістю корпоративного управління та оцінки банку. Емпірична методологія, розроблена в даній статті може бути додатково використаний в дослідженнях; вивчення взаємозв'язку між якістю корпоративного управління і вартістю банку при оптимальному співвідношенні концентрації власності є ще однією перспективною галуззю дослідження