1.
sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.
Wen, B, Xu, S, Sheynkman, GM, Feng, Q, Lin, L, Wang, Q, Xu, X, Wang, J, Liu, S
Bioinformatics (Oxford, England). 2014;(21):3136-8
-
-
Free full text
-
Abstract
UNLABELLED Single nucleotide variations (SNVs) located within a reading frame can result in single amino acid polymorphisms (SAPs), leading to alteration of the corresponding amino acid sequence as well as function of a protein. Accurate detection of SAPs is an important issue in proteomic analysis at the experimental and bioinformatic level. Herein, we present sapFinder, an R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. This package automates the construction of variation-associated databases from public SNV repositories or sample-specific next-generation sequencing (NGS) data and the identification of SAPs through database searching, post-processing and generation of HTML-based report with visualized interface. AVAILABILITY AND IMPLEMENTATION sapFinder is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at http://bioconductor.org/packages/devel/bioc/html/sapFinder.html and are provided under a GPL-2 license.
2.
Alteration of DBP levels in CSF of patients with MS by proteomics analysis.
Qin, Z, Qin, Y, Liu, S
Cellular and molecular neurobiology. 2009;(2):203-10
Abstract
OBJECTIVE The diagnosis of multiple sclerosis (MS) is still challenging recently due to the lack of a specific diagnostic test. Proteomics analysis was applied to biomarkers discovery and their pathways study. METHODS First, the proteins of CSF from MS patients and control group were analyzed individually with 2D-DIGE technology (two-dimensional difference gel electrophoresis). Then, protein spots were found out with DeCyder6.0 software which showed different expression levels in the gel images between the two groups. The information regarding these proteins was collected based on MALDI-TOF/MS and related database searches. Lastly, interaction between these proteins was further analyzed by using Metacore software. RESULTS There were 13 proteins that showed more than 1.5-fold difference in expression levels between the two groups. Furthermore, the identification made by MALDI-TOF/MS revealed that one of the most significant differential proteins was DBP (vitamin D-binding protein), which decreased in the experimental group. This result was confirmed by ELISA (P < 0.01). Moreover, network between the 13 proteins were partially got, which showed some biological interactions. CONCLUSION These results support a correlation between the level of DBP and MS. DBP may be a potential useful biomarker for diagnosis or a medicine target for treatment of MS.