Identification of Alternative Splice Variants Using Unique Tryptic Peptide Sequences for Database Searches

Journal of Proteome Research
Trung T TranBernd Thiede

Abstract

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.

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Citations

Jan 25, 2019·Current Protein & Peptide Science·Alla P Toropova, Andrey A Toropov
Mar 17, 2020·Molecular Systems Biology·Barbora SalovskaYansheng Liu
Dec 13, 2017·International Journal of Molecular Sciences·Xiuquan DuYanping Zhang
Jan 4, 2022·Wiley Interdisciplinary Reviews. RNA·Marina Reixachs-Solé, Eduardo Eyras

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