2 research outputs found
Identification of Alternative Splice Variants Using Unique Tryptic Peptide Sequences for Database Searches
Alternative
splicing is a mechanism in eukaryotes by which different
forms of mRNAs are generated from the same gene. Identification of
alternative splice variants requires the identification of peptides
specific for alternative splice forms. For this purpose, we generated
a human database that contains only unique tryptic peptides specific
for alternative splice forms from Swiss-Prot entries. Using this database
allows an easy access to splice variant-specific peptide sequences
that match to MS data. Furthermore, we combined this database without
alternative splice variant-1-specific peptides with human Swiss-Prot.
This combined database can be used as a general database for searching
of LC–MS data. LC–MS data derived from in-solution digests
of two different cell lines (LNCaP, HeLa) and phosphoproteomics studies
were analyzed using these two databases. Several nonalternative splice
variant-1-specific peptides were found in both cell lines, and some
of them seemed to be cell-line-specific. Control and apoptotic phosphoproteomes
from Jurkat T cells revealed several nonalternative splice variant-1-specific
peptides, and some of them showed clear quantitative differences between
the two states
Identification of Alternative Splice Variants Using Unique Tryptic Peptide Sequences for Database Searches
Alternative
splicing is a mechanism in eukaryotes by which different
forms of mRNAs are generated from the same gene. Identification of
alternative splice variants requires the identification of peptides
specific for alternative splice forms. For this purpose, we generated
a human database that contains only unique tryptic peptides specific
for alternative splice forms from Swiss-Prot entries. Using this database
allows an easy access to splice variant-specific peptide sequences
that match to MS data. Furthermore, we combined this database without
alternative splice variant-1-specific peptides with human Swiss-Prot.
This combined database can be used as a general database for searching
of LC–MS data. LC–MS data derived from in-solution digests
of two different cell lines (LNCaP, HeLa) and phosphoproteomics studies
were analyzed using these two databases. Several nonalternative splice
variant-1-specific peptides were found in both cell lines, and some
of them seemed to be cell-line-specific. Control and apoptotic phosphoproteomes
from Jurkat T cells revealed several nonalternative splice variant-1-specific
peptides, and some of them showed clear quantitative differences between
the two states