8 research outputs found
concatenated plastid data
Concatenated four plastid regions of Fagus, including trnK-matK, trnL-trnF, trnH-psbA, and atpB-rbcL region
Proteogenomic Study beyond Chromosome 9: New Insight into Expressed Variant Proteome and Transcriptome in Human Lung Adenocarcinoma Tissues
This
is a report of a human proteome project (HPP) related to chromosome
9 (Chr 9). To reveal missing proteins and undiscovered features in
proteogenomes, both LC–MS/MS analysis and next-generation RNA
sequencing (RNA-seq)-based identification and characterization were
conducted on five pairs of lung adenocarcinoma tumors and adjacent
nontumor tissues. Before our previous Chromosome-Centric Human Proteome
Project (C-HPP) special issue, there were 170 remaining missing proteins
on Chr 9 (neXtProt 2013.09.26 rel.); 133 remain at present (neXtProt
2015.04.28 rel.). In the proteomics study, we found two missing protein
candidates that require follow-up work and one unrevealed protein
across all chromosomes. RNA-seq analysis detected RNA expression for
four nonsynonymous (NS) single nucleotide polymorphisms (SNPs) (in
CDH17, HIST1H1T, SAPCD2, and ZNF695) and three synonymous SNPs (in
CDH17, CST1, and HNF1A) in all five tumor tissues but not in any of
the adjacent normal tissues. By constructing a cancer patient sample-specific
protein database based on individual RNA-seq data and by searching
the proteomics data from the same sample, we identified four missense
mutations in four genes (LTF, HDLBP, TF, and HBD). Two of these mutations
were found in tumor samples but not in paired normal tissues. In summary,
our proteogenomic study of human primary lung tumor tissues detected
additional and revealed novel missense mutations and synonymous SNP
signatures, some of which are specific to lung cancers. Data from
mass spectrometry have been deposited in the ProteomeXchange with
the identifier PXD002523
Proteogenomic Analysis of Human Chromosome 9‑Encoded Genes from Human Samples and Lung Cancer Tissues
The Chromosome-centric Human Proteome
Project (C-HPP) was recently
initiated as an international collaborative effort. Our team adopted
chromosome 9 (Chr 9) and performed a bioinformatics and proteogenomic
analysis to catalog Chr 9-encoded proteins from normal tissues, lung
cancer cell lines, and lung cancer tissues. Approximately 74.7% of
the Chr 9 genes of the human genome were identified, which included
approximately 28% of missing proteins (46 of 162) on Chr 9 compared
with the list of missing proteins from the neXtProt Master Table (2013-09).
In addition, we performed a comparative proteomics analysis between
normal lung and lung cancer tissues. On the basis of the data analysis,
15 proteins from Chr 9 were detected only in lung cancer tissues.
Finally, we conducted a proteogenomic analysis to discover Chr 9-residing
single nucleotide polymorphisms (SNP) and mutations described in the
COSMIC cancer mutation database. We identified 21 SNPs and four mutations
containing peptides on Chr 9 from normal human cells/tissues and lung
cancer cell lines, respectively. In summary, this study provides valuable
information of the human proteome for the scientific community as
part of C-HPP. The mass spectrometry proteomics data have been deposited
to the ProteomeXchange Consortium with the data set identifier PXD000603
Proteogenomic Analysis of Human Chromosome 9‑Encoded Genes from Human Samples and Lung Cancer Tissues
The Chromosome-centric Human Proteome
Project (C-HPP) was recently
initiated as an international collaborative effort. Our team adopted
chromosome 9 (Chr 9) and performed a bioinformatics and proteogenomic
analysis to catalog Chr 9-encoded proteins from normal tissues, lung
cancer cell lines, and lung cancer tissues. Approximately 74.7% of
the Chr 9 genes of the human genome were identified, which included
approximately 28% of missing proteins (46 of 162) on Chr 9 compared
with the list of missing proteins from the neXtProt Master Table (2013-09).
In addition, we performed a comparative proteomics analysis between
normal lung and lung cancer tissues. On the basis of the data analysis,
15 proteins from Chr 9 were detected only in lung cancer tissues.
Finally, we conducted a proteogenomic analysis to discover Chr 9-residing
single nucleotide polymorphisms (SNP) and mutations described in the
COSMIC cancer mutation database. We identified 21 SNPs and four mutations
containing peptides on Chr 9 from normal human cells/tissues and lung
cancer cell lines, respectively. In summary, this study provides valuable
information of the human proteome for the scientific community as
part of C-HPP. The mass spectrometry proteomics data have been deposited
to the ProteomeXchange Consortium with the data set identifier PXD000603
Proteogenomic Analysis of Human Chromosome 9‑Encoded Genes from Human Samples and Lung Cancer Tissues
The Chromosome-centric Human Proteome
Project (C-HPP) was recently
initiated as an international collaborative effort. Our team adopted
chromosome 9 (Chr 9) and performed a bioinformatics and proteogenomic
analysis to catalog Chr 9-encoded proteins from normal tissues, lung
cancer cell lines, and lung cancer tissues. Approximately 74.7% of
the Chr 9 genes of the human genome were identified, which included
approximately 28% of missing proteins (46 of 162) on Chr 9 compared
with the list of missing proteins from the neXtProt Master Table (2013-09).
In addition, we performed a comparative proteomics analysis between
normal lung and lung cancer tissues. On the basis of the data analysis,
15 proteins from Chr 9 were detected only in lung cancer tissues.
Finally, we conducted a proteogenomic analysis to discover Chr 9-residing
single nucleotide polymorphisms (SNP) and mutations described in the
COSMIC cancer mutation database. We identified 21 SNPs and four mutations
containing peptides on Chr 9 from normal human cells/tissues and lung
cancer cell lines, respectively. In summary, this study provides valuable
information of the human proteome for the scientific community as
part of C-HPP. The mass spectrometry proteomics data have been deposited
to the ProteomeXchange Consortium with the data set identifier PXD000603
Proteogenomic Analysis of Human Chromosome 9‑Encoded Genes from Human Samples and Lung Cancer Tissues
The Chromosome-centric Human Proteome
Project (C-HPP) was recently
initiated as an international collaborative effort. Our team adopted
chromosome 9 (Chr 9) and performed a bioinformatics and proteogenomic
analysis to catalog Chr 9-encoded proteins from normal tissues, lung
cancer cell lines, and lung cancer tissues. Approximately 74.7% of
the Chr 9 genes of the human genome were identified, which included
approximately 28% of missing proteins (46 of 162) on Chr 9 compared
with the list of missing proteins from the neXtProt Master Table (2013-09).
In addition, we performed a comparative proteomics analysis between
normal lung and lung cancer tissues. On the basis of the data analysis,
15 proteins from Chr 9 were detected only in lung cancer tissues.
Finally, we conducted a proteogenomic analysis to discover Chr 9-residing
single nucleotide polymorphisms (SNP) and mutations described in the
COSMIC cancer mutation database. We identified 21 SNPs and four mutations
containing peptides on Chr 9 from normal human cells/tissues and lung
cancer cell lines, respectively. In summary, this study provides valuable
information of the human proteome for the scientific community as
part of C-HPP. The mass spectrometry proteomics data have been deposited
to the ProteomeXchange Consortium with the data set identifier PXD000603
Characterization of Site-Specific <i>N</i>‑Glycopeptide Isoforms of α‑1-Acid Glycoprotein from an Interlaboratory Study Using LC–MS/MS
Glycoprotein conformations are complex and heterogeneous. Currently,
site-specific characterization of glycopeptides is a challenge. We
sought to establish an efficient method of <i>N</i>-glycoprotein
characterization using mass spectrometry (MS). Using alpha-1-acid
glycoprotein (AGP) as a model <i>N</i>-glycoprotein, we
identified its tryptic <i>N</i>-glycopeptides and examined
the data reproducibility in seven laboratories running different LC–MS/MS
platforms. We used three test samples and one blind sample to evaluate
instrument performance with entire sample preparation workflow. 165
site-specific <i>N</i>-glycopeptides representative of all <i>N</i>-glycosylation sites were identified from AGP 1 and AGP 2 isoforms. The glycopeptide fragmentations by collision-induced dissociation or higher-energy collisional dissociation (HCD) varied based on the MS analyzer. Orbitrap Elite identified the greatest number of AGP <i>N</i>-glycopeptides, followed by Triple TOF and Q-Exactive Plus. Reproducible generation of oxonium ions, glycan-cleaved glycopeptide fragment ions, and peptide backbone fragment ions was essential for successful identification. Laboratory proficiency affected the number of identified <i>N</i>-glycopeptides. The relative quantities of the 10 major <i>N</i>-glycopeptide isoforms of AGP detected in four laboratories were compared to assess reproducibility. Quantitative analysis showed that the coefficient of variation was <25% for all test samples. Our analytical protocol yielded identification and quantification of site-specific <i>N</i>-glycopeptide isoforms of AGP from control and disease plasma sample