13 research outputs found
Chromosome 19 Annotations with Disease Speciation: A First Report from the Global Research Consortium
A first research development progress report of the Chromosome
19 Consortium with members from Sweden, Norway, Spain, United States,
China and India, a part of the Chromosome-centric Human Proteome Project
(C-HPP) global initiative, is presented (http://www.c-hpp.org). From the chromosome 19 peptide-targeted library constituting 6159
peptides, a pilot study was conducted using a subset with 125 isotope-labeled
peptides. We applied an annotation strategy with triple quadrupole,
ESI-Qtrap, and MALDI mass spectrometry platforms, comparing the quality
of data within and in between these instrumental set-ups. LC–MS
conditions were outlined by multiplex assay developments, followed
by MRM assay developments. SRM was applied to biobank samples, quantifying
kallikrein 3 (prostate specific antigen) in plasma from prostate cancer
patients. The antibody production has been initiated for more than
1200 genes from the entire chromosome 19, and the progress developments
are presented. We developed a dedicated transcript microarray to serve
as the mRNA identifier by screening cancer cell lines. NAPPA protein
arrays were built to align with the transcript data with the Chromosome
19 NAPPA chip, dedicated to 90 proteins, as the first development
delivery. We have introduced an IT-infrastructure utilizing a LIMS
system that serves as the key interface for the research teams to
share and explore data generated within the project. The cross-site
data repository will form the basis for sample processing, including
biological samples as well as patient samples from national Biobanks
Chromosome 19 Annotations with Disease Speciation: A First Report from the Global Research Consortium
A first research development progress report of the Chromosome
19 Consortium with members from Sweden, Norway, Spain, United States,
China and India, a part of the Chromosome-centric Human Proteome Project
(C-HPP) global initiative, is presented (http://www.c-hpp.org). From the chromosome 19 peptide-targeted library constituting 6159
peptides, a pilot study was conducted using a subset with 125 isotope-labeled
peptides. We applied an annotation strategy with triple quadrupole,
ESI-Qtrap, and MALDI mass spectrometry platforms, comparing the quality
of data within and in between these instrumental set-ups. LC–MS
conditions were outlined by multiplex assay developments, followed
by MRM assay developments. SRM was applied to biobank samples, quantifying
kallikrein 3 (prostate specific antigen) in plasma from prostate cancer
patients. The antibody production has been initiated for more than
1200 genes from the entire chromosome 19, and the progress developments
are presented. We developed a dedicated transcript microarray to serve
as the mRNA identifier by screening cancer cell lines. NAPPA protein
arrays were built to align with the transcript data with the Chromosome
19 NAPPA chip, dedicated to 90 proteins, as the first development
delivery. We have introduced an IT-infrastructure utilizing a LIMS
system that serves as the key interface for the research teams to
share and explore data generated within the project. The cross-site
data repository will form the basis for sample processing, including
biological samples as well as patient samples from national Biobanks
Chromosome 19 Annotations with Disease Speciation: A First Report from the Global Research Consortium
A first research development progress report of the Chromosome
19 Consortium with members from Sweden, Norway, Spain, United States,
China and India, a part of the Chromosome-centric Human Proteome Project
(C-HPP) global initiative, is presented (http://www.c-hpp.org). From the chromosome 19 peptide-targeted library constituting 6159
peptides, a pilot study was conducted using a subset with 125 isotope-labeled
peptides. We applied an annotation strategy with triple quadrupole,
ESI-Qtrap, and MALDI mass spectrometry platforms, comparing the quality
of data within and in between these instrumental set-ups. LC–MS
conditions were outlined by multiplex assay developments, followed
by MRM assay developments. SRM was applied to biobank samples, quantifying
kallikrein 3 (prostate specific antigen) in plasma from prostate cancer
patients. The antibody production has been initiated for more than
1200 genes from the entire chromosome 19, and the progress developments
are presented. We developed a dedicated transcript microarray to serve
as the mRNA identifier by screening cancer cell lines. NAPPA protein
arrays were built to align with the transcript data with the Chromosome
19 NAPPA chip, dedicated to 90 proteins, as the first development
delivery. We have introduced an IT-infrastructure utilizing a LIMS
system that serves as the key interface for the research teams to
share and explore data generated within the project. The cross-site
data repository will form the basis for sample processing, including
biological samples as well as patient samples from national Biobanks
Chromosome 19 Annotations with Disease Speciation: A First Report from the Global Research Consortium
A first research development progress report of the Chromosome
19 Consortium with members from Sweden, Norway, Spain, United States,
China and India, a part of the Chromosome-centric Human Proteome Project
(C-HPP) global initiative, is presented (http://www.c-hpp.org). From the chromosome 19 peptide-targeted library constituting 6159
peptides, a pilot study was conducted using a subset with 125 isotope-labeled
peptides. We applied an annotation strategy with triple quadrupole,
ESI-Qtrap, and MALDI mass spectrometry platforms, comparing the quality
of data within and in between these instrumental set-ups. LC–MS
conditions were outlined by multiplex assay developments, followed
by MRM assay developments. SRM was applied to biobank samples, quantifying
kallikrein 3 (prostate specific antigen) in plasma from prostate cancer
patients. The antibody production has been initiated for more than
1200 genes from the entire chromosome 19, and the progress developments
are presented. We developed a dedicated transcript microarray to serve
as the mRNA identifier by screening cancer cell lines. NAPPA protein
arrays were built to align with the transcript data with the Chromosome
19 NAPPA chip, dedicated to 90 proteins, as the first development
delivery. We have introduced an IT-infrastructure utilizing a LIMS
system that serves as the key interface for the research teams to
share and explore data generated within the project. The cross-site
data repository will form the basis for sample processing, including
biological samples as well as patient samples from national Biobanks
Surfing Transcriptomic Landscapes. A Step beyond the Annotation of Chromosome 16 Proteome
The
Spanish team of the Human Proteome Project (SpHPP) marked the
annotation of Chr16 and data analysis as one of its priorities. Precise
annotation of Chromosome 16 proteins according to C-HPP criteria is
presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of
DNA Elements (ENCODE) data sets were used to obtain further information
relative to cell/tissue specific chromosome 16 coding gene expression
patterns and to infer the presence of missing proteins. Twenty-four
shotgun 2D-LC–MS/MS and gel/LC–MS/MS MIAPE compliant
experiments, representing 41% coverage of chromosome 16 proteins,
were performed. Furthermore, mapping of large-scale multicenter mass
spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines
into RNA-Seq data allowed further insights relative to correlation
of chromosome 16 transcripts and proteins. Detection and quantification
of chromosome 16 proteins in biological matrices by SRM procedures
are also primary goals of the SpHPP. Two strategies were undertaken:
one focused on known proteins, taking advantage of MS data already
available, and the second, aimed at the detection of the missing proteins,
is based on the expression of recombinant proteins to gather MS information
and optimize SRM methods that will be used in real biological samples.
SRM methods for 49 known proteins and for recombinant forms of 24
missing proteins are reported in this study
Surfing Transcriptomic Landscapes. A Step beyond the Annotation of Chromosome 16 Proteome
The
Spanish team of the Human Proteome Project (SpHPP) marked the
annotation of Chr16 and data analysis as one of its priorities. Precise
annotation of Chromosome 16 proteins according to C-HPP criteria is
presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of
DNA Elements (ENCODE) data sets were used to obtain further information
relative to cell/tissue specific chromosome 16 coding gene expression
patterns and to infer the presence of missing proteins. Twenty-four
shotgun 2D-LC–MS/MS and gel/LC–MS/MS MIAPE compliant
experiments, representing 41% coverage of chromosome 16 proteins,
were performed. Furthermore, mapping of large-scale multicenter mass
spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines
into RNA-Seq data allowed further insights relative to correlation
of chromosome 16 transcripts and proteins. Detection and quantification
of chromosome 16 proteins in biological matrices by SRM procedures
are also primary goals of the SpHPP. Two strategies were undertaken:
one focused on known proteins, taking advantage of MS data already
available, and the second, aimed at the detection of the missing proteins,
is based on the expression of recombinant proteins to gather MS information
and optimize SRM methods that will be used in real biological samples.
SRM methods for 49 known proteins and for recombinant forms of 24
missing proteins are reported in this study
Surfing Transcriptomic Landscapes. A Step beyond the Annotation of Chromosome 16 Proteome
The
Spanish team of the Human Proteome Project (SpHPP) marked the
annotation of Chr16 and data analysis as one of its priorities. Precise
annotation of Chromosome 16 proteins according to C-HPP criteria is
presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of
DNA Elements (ENCODE) data sets were used to obtain further information
relative to cell/tissue specific chromosome 16 coding gene expression
patterns and to infer the presence of missing proteins. Twenty-four
shotgun 2D-LC–MS/MS and gel/LC–MS/MS MIAPE compliant
experiments, representing 41% coverage of chromosome 16 proteins,
were performed. Furthermore, mapping of large-scale multicenter mass
spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines
into RNA-Seq data allowed further insights relative to correlation
of chromosome 16 transcripts and proteins. Detection and quantification
of chromosome 16 proteins in biological matrices by SRM procedures
are also primary goals of the SpHPP. Two strategies were undertaken:
one focused on known proteins, taking advantage of MS data already
available, and the second, aimed at the detection of the missing proteins,
is based on the expression of recombinant proteins to gather MS information
and optimize SRM methods that will be used in real biological samples.
SRM methods for 49 known proteins and for recombinant forms of 24
missing proteins are reported in this study
Surfing Transcriptomic Landscapes. A Step beyond the Annotation of Chromosome 16 Proteome
The
Spanish team of the Human Proteome Project (SpHPP) marked the
annotation of Chr16 and data analysis as one of its priorities. Precise
annotation of Chromosome 16 proteins according to C-HPP criteria is
presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of
DNA Elements (ENCODE) data sets were used to obtain further information
relative to cell/tissue specific chromosome 16 coding gene expression
patterns and to infer the presence of missing proteins. Twenty-four
shotgun 2D-LC–MS/MS and gel/LC–MS/MS MIAPE compliant
experiments, representing 41% coverage of chromosome 16 proteins,
were performed. Furthermore, mapping of large-scale multicenter mass
spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines
into RNA-Seq data allowed further insights relative to correlation
of chromosome 16 transcripts and proteins. Detection and quantification
of chromosome 16 proteins in biological matrices by SRM procedures
are also primary goals of the SpHPP. Two strategies were undertaken:
one focused on known proteins, taking advantage of MS data already
available, and the second, aimed at the detection of the missing proteins,
is based on the expression of recombinant proteins to gather MS information
and optimize SRM methods that will be used in real biological samples.
SRM methods for 49 known proteins and for recombinant forms of 24
missing proteins are reported in this study
Surfing Transcriptomic Landscapes. A Step beyond the Annotation of Chromosome 16 Proteome
The
Spanish team of the Human Proteome Project (SpHPP) marked the
annotation of Chr16 and data analysis as one of its priorities. Precise
annotation of Chromosome 16 proteins according to C-HPP criteria is
presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of
DNA Elements (ENCODE) data sets were used to obtain further information
relative to cell/tissue specific chromosome 16 coding gene expression
patterns and to infer the presence of missing proteins. Twenty-four
shotgun 2D-LC–MS/MS and gel/LC–MS/MS MIAPE compliant
experiments, representing 41% coverage of chromosome 16 proteins,
were performed. Furthermore, mapping of large-scale multicenter mass
spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines
into RNA-Seq data allowed further insights relative to correlation
of chromosome 16 transcripts and proteins. Detection and quantification
of chromosome 16 proteins in biological matrices by SRM procedures
are also primary goals of the SpHPP. Two strategies were undertaken:
one focused on known proteins, taking advantage of MS data already
available, and the second, aimed at the detection of the missing proteins,
is based on the expression of recombinant proteins to gather MS information
and optimize SRM methods that will be used in real biological samples.
SRM methods for 49 known proteins and for recombinant forms of 24
missing proteins are reported in this study
Surfing Transcriptomic Landscapes. A Step beyond the Annotation of Chromosome 16 Proteome
The
Spanish team of the Human Proteome Project (SpHPP) marked the
annotation of Chr16 and data analysis as one of its priorities. Precise
annotation of Chromosome 16 proteins according to C-HPP criteria is
presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of
DNA Elements (ENCODE) data sets were used to obtain further information
relative to cell/tissue specific chromosome 16 coding gene expression
patterns and to infer the presence of missing proteins. Twenty-four
shotgun 2D-LC–MS/MS and gel/LC–MS/MS MIAPE compliant
experiments, representing 41% coverage of chromosome 16 proteins,
were performed. Furthermore, mapping of large-scale multicenter mass
spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines
into RNA-Seq data allowed further insights relative to correlation
of chromosome 16 transcripts and proteins. Detection and quantification
of chromosome 16 proteins in biological matrices by SRM procedures
are also primary goals of the SpHPP. Two strategies were undertaken:
one focused on known proteins, taking advantage of MS data already
available, and the second, aimed at the detection of the missing proteins,
is based on the expression of recombinant proteins to gather MS information
and optimize SRM methods that will be used in real biological samples.
SRM methods for 49 known proteins and for recombinant forms of 24
missing proteins are reported in this study