31 research outputs found
Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides
Protein glycosylation plays fundamental
roles in many cellular processes, and previous reports have shown
dysregulation to be associated with several human diseases, including
diabetes, cancer, and neurodegenerative disorders. Despite the vital
role of glycosylation for proper protein function, the analysis of
glycoproteins has been lagged behind to other protein modifications.
In this study, we describe the reanalysis of global proteomic data
from breast cancer xenograft tissues using recently developed software
package GPQuest 2.0, revealing a large number of previously unidentified
N-linked glycopeptides. More importantly, we found that using immobilized
metal affinity chromatography (IMAC) technology for the enrichment
of phosphopeptides had coenriched a substantial number of sialoglycopeptides,
allowing for a large-scale analysis of sialoglycopeptides in conjunction
with the analysis of phosphopeptides. Collectively, combined tandem
mass spectrometry (MS/MS) analyses of global proteomic and phosphoproteomic
data sets resulted in the identification of 6 724 N-linked
glycopeptides from 617 glycoproteins derived from two breast cancer
xenograft tissues. Next, we utilized GPQuest 2.0 for the reanalysis
of global and phosphoproteomic data generated from 108 human breast
cancer tissues that were previously analyzed by Clinical Proteomic
Analysis Consortium (CPTAC). Reanalysis of the CPTAC data set resulted
in the identification of 2 683 glycopeptides from the global
proteomic data set and 4 554 glycopeptides from phosphoproteomic
data set, respectively. Together, 11 292 N-linked glycopeptides
corresponding to 1 731 N-linked glycosites from 883 human glycoproteins
were identified from the two data sets. This analysis revealed an
extensive number of glycopeptides hidden in the global and enriched
in IMAC-based phosphopeptide-enriched proteomic data, information
which would have remained unknown from the original study otherwise.
The reanalysis described herein can be readily applied to identify
glycopeptides from already existing data sets, providing insight into
many important facets of protein glycosylation in different biological,
physiological, and pathological processes
Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides
Protein glycosylation plays fundamental
roles in many cellular processes, and previous reports have shown
dysregulation to be associated with several human diseases, including
diabetes, cancer, and neurodegenerative disorders. Despite the vital
role of glycosylation for proper protein function, the analysis of
glycoproteins has been lagged behind to other protein modifications.
In this study, we describe the reanalysis of global proteomic data
from breast cancer xenograft tissues using recently developed software
package GPQuest 2.0, revealing a large number of previously unidentified
N-linked glycopeptides. More importantly, we found that using immobilized
metal affinity chromatography (IMAC) technology for the enrichment
of phosphopeptides had coenriched a substantial number of sialoglycopeptides,
allowing for a large-scale analysis of sialoglycopeptides in conjunction
with the analysis of phosphopeptides. Collectively, combined tandem
mass spectrometry (MS/MS) analyses of global proteomic and phosphoproteomic
data sets resulted in the identification of 6 724 N-linked
glycopeptides from 617 glycoproteins derived from two breast cancer
xenograft tissues. Next, we utilized GPQuest 2.0 for the reanalysis
of global and phosphoproteomic data generated from 108 human breast
cancer tissues that were previously analyzed by Clinical Proteomic
Analysis Consortium (CPTAC). Reanalysis of the CPTAC data set resulted
in the identification of 2 683 glycopeptides from the global
proteomic data set and 4 554 glycopeptides from phosphoproteomic
data set, respectively. Together, 11 292 N-linked glycopeptides
corresponding to 1 731 N-linked glycosites from 883 human glycoproteins
were identified from the two data sets. This analysis revealed an
extensive number of glycopeptides hidden in the global and enriched
in IMAC-based phosphopeptide-enriched proteomic data, information
which would have remained unknown from the original study otherwise.
The reanalysis described herein can be readily applied to identify
glycopeptides from already existing data sets, providing insight into
many important facets of protein glycosylation in different biological,
physiological, and pathological processes
Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides
Protein glycosylation plays fundamental
roles in many cellular processes, and previous reports have shown
dysregulation to be associated with several human diseases, including
diabetes, cancer, and neurodegenerative disorders. Despite the vital
role of glycosylation for proper protein function, the analysis of
glycoproteins has been lagged behind to other protein modifications.
In this study, we describe the reanalysis of global proteomic data
from breast cancer xenograft tissues using recently developed software
package GPQuest 2.0, revealing a large number of previously unidentified
N-linked glycopeptides. More importantly, we found that using immobilized
metal affinity chromatography (IMAC) technology for the enrichment
of phosphopeptides had coenriched a substantial number of sialoglycopeptides,
allowing for a large-scale analysis of sialoglycopeptides in conjunction
with the analysis of phosphopeptides. Collectively, combined tandem
mass spectrometry (MS/MS) analyses of global proteomic and phosphoproteomic
data sets resulted in the identification of 6 724 N-linked
glycopeptides from 617 glycoproteins derived from two breast cancer
xenograft tissues. Next, we utilized GPQuest 2.0 for the reanalysis
of global and phosphoproteomic data generated from 108 human breast
cancer tissues that were previously analyzed by Clinical Proteomic
Analysis Consortium (CPTAC). Reanalysis of the CPTAC data set resulted
in the identification of 2 683 glycopeptides from the global
proteomic data set and 4 554 glycopeptides from phosphoproteomic
data set, respectively. Together, 11 292 N-linked glycopeptides
corresponding to 1 731 N-linked glycosites from 883 human glycoproteins
were identified from the two data sets. This analysis revealed an
extensive number of glycopeptides hidden in the global and enriched
in IMAC-based phosphopeptide-enriched proteomic data, information
which would have remained unknown from the original study otherwise.
The reanalysis described herein can be readily applied to identify
glycopeptides from already existing data sets, providing insight into
many important facets of protein glycosylation in different biological,
physiological, and pathological processes
Relationships between GVI (vertical axis) and EGVI, in the data from Gouelle et al. (2013).
<p>Relationships between GVI (vertical axis) and EGVI, in the data from Gouelle et al. (2013).</p
Addressing limitations of the Gait Variability Index to enhance its applicability: The enhanced GVI (EGVI) - Fig 4
<p><b>Relationships between GVI (vertical axis) and EGVI, in the data from Balasubramanian et al. (2016) (4a) and in the data from Rennie et al. (2017) (4b).</b> The coefficient of determination was computed once all data represented by crosses were removed. The crosses in the area where GVI<100 and EGVI<100 correspond to data for which the lower GVI was due to lower variability than HP. The crosses for GVI>100 are from individuals whose distance <i>d</i><sup><i>⍺</i>,<i>HP</i></sup> was smaller than mean HP.</p
Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides
Protein glycosylation plays fundamental
roles in many cellular processes, and previous reports have shown
dysregulation to be associated with several human diseases, including
diabetes, cancer, and neurodegenerative disorders. Despite the vital
role of glycosylation for proper protein function, the analysis of
glycoproteins has been lagged behind to other protein modifications.
In this study, we describe the reanalysis of global proteomic data
from breast cancer xenograft tissues using recently developed software
package GPQuest 2.0, revealing a large number of previously unidentified
N-linked glycopeptides. More importantly, we found that using immobilized
metal affinity chromatography (IMAC) technology for the enrichment
of phosphopeptides had coenriched a substantial number of sialoglycopeptides,
allowing for a large-scale analysis of sialoglycopeptides in conjunction
with the analysis of phosphopeptides. Collectively, combined tandem
mass spectrometry (MS/MS) analyses of global proteomic and phosphoproteomic
data sets resulted in the identification of 6 724 N-linked
glycopeptides from 617 glycoproteins derived from two breast cancer
xenograft tissues. Next, we utilized GPQuest 2.0 for the reanalysis
of global and phosphoproteomic data generated from 108 human breast
cancer tissues that were previously analyzed by Clinical Proteomic
Analysis Consortium (CPTAC). Reanalysis of the CPTAC data set resulted
in the identification of 2 683 glycopeptides from the global
proteomic data set and 4 554 glycopeptides from phosphoproteomic
data set, respectively. Together, 11 292 N-linked glycopeptides
corresponding to 1 731 N-linked glycosites from 883 human glycoproteins
were identified from the two data sets. This analysis revealed an
extensive number of glycopeptides hidden in the global and enriched
in IMAC-based phosphopeptide-enriched proteomic data, information
which would have remained unknown from the original study otherwise.
The reanalysis described herein can be readily applied to identify
glycopeptides from already existing data sets, providing insight into
many important facets of protein glycosylation in different biological,
physiological, and pathological processes
Description of data sets re-analyzed in the current study.
<p>Description of data sets re-analyzed in the current study.</p
Relationships between GVI (vertical axis) and EGVI, in the data from Gouelle et al. (2015).
<p>The point in dark green represents the younger child who walked independently only for two weeks and is provided to give an idea about what could be about the ceiling of EGVI (175) for a high level of unsteadiness in ambulation.</p
Evaluation of NCI‑7 Cell Line Panel as a Reference Material for Clinical Proteomics
Reference materials are vital to
benchmarking the reproducibility
of clinical tests and essential for monitoring laboratory performance
for clinical proteomics. The reference material utilized for mass
spectrometric analysis of the human proteome would ideally contain
enough proteins to be suitably representative of the human proteome,
as well as exhibit a stable protein composition in different batches
of sample regeneration. Previously, The Clinical Proteomic Tumor Analysis
Consortium (CPTAC) utilized a PDX-derived comparative reference (CompRef)
materials for the longitudinal assessment of proteomic performance;
however, inherent drawbacks of PDX-derived material, including extended
time needed to grow tumors and high level of expertise needed, have
resulted in efforts to identify a new source of CompRef material.
In this study, we examined the utility of using a panel of seven cancer
cell lines, NCI-7 Cell Line Panel, as a reference material for mass
spectrometric analysis of human proteome. Our results showed that
not only is the NCI-7 material suitable for benchmarking laboratory
sample preparation methods, but also NCI-7 sample generation is highly
reproducible at both the global and phosphoprotein levels. In addition,
the predicted genomic and experimental coverage of the NCI-7 proteome
suggests the NCI-7 material may also have applications as a universal
standard proteomic reference
Evaluation of NCI‑7 Cell Line Panel as a Reference Material for Clinical Proteomics
Reference materials are vital to
benchmarking the reproducibility
of clinical tests and essential for monitoring laboratory performance
for clinical proteomics. The reference material utilized for mass
spectrometric analysis of the human proteome would ideally contain
enough proteins to be suitably representative of the human proteome,
as well as exhibit a stable protein composition in different batches
of sample regeneration. Previously, The Clinical Proteomic Tumor Analysis
Consortium (CPTAC) utilized a PDX-derived comparative reference (CompRef)
materials for the longitudinal assessment of proteomic performance;
however, inherent drawbacks of PDX-derived material, including extended
time needed to grow tumors and high level of expertise needed, have
resulted in efforts to identify a new source of CompRef material.
In this study, we examined the utility of using a panel of seven cancer
cell lines, NCI-7 Cell Line Panel, as a reference material for mass
spectrometric analysis of human proteome. Our results showed that
not only is the NCI-7 material suitable for benchmarking laboratory
sample preparation methods, but also NCI-7 sample generation is highly
reproducible at both the global and phosphoprotein levels. In addition,
the predicted genomic and experimental coverage of the NCI-7 proteome
suggests the NCI-7 material may also have applications as a universal
standard proteomic reference