13 research outputs found
A molecular basis for the presentation of phosphorylated peptides by HLA-B antigens (ANNOTATED MS2 SPECTRA OF PHOSPHOPEPTIDES)
<p>Phosphopeptides identified from the immunopeptidome of the C1R-B*40 cell line. </p>
<p>Phosphopeptides identified from the proteome of the C1R-B*40 cell line. </p>
<p>Phosphopeptides identified from the immunopeptidome of the GR cell line. </p
Comparative Analysis of the Endogenous Peptidomes Displayed by HLA-B*27 and Mamu-B*08: Two MHC Class I Alleles Associated with Elite Control of HIV/SIV Infection
Indian
rhesus macaques are arguably the most reliable animal models
in AIDS research. In this species the MHC class I allele Mamu-B*08,
among others, is associated with elite control of SIV replication.
A similar scenario is observed in humans where the expression of HLA-B*27
or HLA-B*57 has been linked to slow or no progression to AIDS after
HIV infection. Despite having large differences in their primary structure,
it has been reported that HLA-B*27 and Mamu-B*08 display peptides
with sequence similarity. To fine-map the Mamu-B*08 binding motif
and assess its similarities with that of HLA-B*27, we affinity purified
the peptidomes bound to these MHC class I molecules and analyzed them
by LC-MS, identifying several thousands of endogenous ligands. Sequence
analysis of both sets of peptides revealed a degree of similarity
in their binding motifs, especially at peptide position 2 (P2), where
arginine was present in the vast majority of ligands of both allotypes.
In addition, several differences emerged from this analysis: (i) ligands
displayed by Mamu-B*08 tended to be shorter and to have lower molecular
weight, (ii) Mamu-B*08 showed a higher preference for glutamine at
P2 as a suboptimal binding motif, and (iii) the second major anchor
position, found at PΩ, was much more restrictive in Mamu-B*08.
In this regard, HLA-B*27 bound efficiently peptides with aliphatic,
aromatic (including tyrosine), and basic C-terminal residues while
Mamu-B*08 preferred peptides with leucine and phenylalanine in this
position. Finally, in silico estimations of binding efficiency and
competitive binding assays to Mamu-B*08 of several selected peptides
revealed a good correlation between the characterized anchor motif
and binding affinity. These results deepen our understanding of the
molecular basis of the presentation of peptides by Mamu-B*08 and can
contribute to the detection of novel SIV epitopes restricted by this
allotype
Identification of the Missing Protein Hyaluronan Synthase 1 in Human Mesenchymal Stem Cells Derived from Adipose Tissue or Umbilical Cord
Currently, 14% of the human proteome
is made up of proteins whose
existence is not confirmed by mass spectrometry. We performed a proteomic
profiling of human mesenchymal stem cells derived from adipose tissue
or umbilical cord (PRIDE accession number: PXD009893) and identified
peptides derived from 13 of such missing proteins. Remarkably, we
found compelling evidence of the expression of hyaluronan synthase
1 (NX_Q92839-1) and confirmed its identification by the fragmentation
of four heavy-labeled peptides that coeluted with their endogenous
light counterparts. Our data also suggest that mesenchymal stem cells
constitute a promising source for the detection of missing proteins
Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach
The Human Proteome
Project (HPP) aims deciphering the complete
map of the human proteome. In the past few years, significant efforts
of the HPP teams have been dedicated to the experimental detection
of the missing proteins, which lack reliable mass spectrometry evidence
of their existence. In this endeavor, an in depth analysis of shotgun
experiments might represent a valuable resource to select a biological
matrix in design validation experiments. In this work, we used all
the proteomic experiments from the NCI60 cell lines and applied an
integrative approach based on the results obtained from Comet, Mascot,
OMSSA, and X!Tandem. This workflow benefits from the complementarity
of these search engines to increase the proteome coverage. Five missing
proteins C-HPP guidelines compliant were identified, although further
validation is needed. Moreover, 165 missing proteins were detected
with only one unique peptide, and their functional analysis supported
their participation in cellular pathways as was also proposed in other
studies. Finally, we performed a combined analysis of the gene expression
levels and the proteomic identifications from the common cell lines
between the NCI60 and the CCLE project to suggest alternatives for
further validation of missing protein observations
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