Source:http://urology.jhu.edu/research/img1/proteomics13.jpg. EAM: Energy. Absorbing. Molecule. Page 8. Preprocessing of MS data. âAlignment of the ...
SELDI-TOF Mass Spectrometry Protein Data By Huong Thi Dieu La
References Alejandro Cruz-Marcelo, Rudy Guerra, Marina Vannucci, Yiting Li, Ching C. Lau, and Tsz-Kwong Man. Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data. Bioinformatics, 24(19):2129–2136, 2008. zRobert Gentleman, Vincent Carey, Wolfgang Huber, Rafael Irizarry, and Sandrine Dudoit. Bioinformatics and Computational Biology Solutions Using R and Bioconductor (Statistics for Biology and Health). Springer Science and Business Media, Inc, New York, first edition edition, 2005. zHaleem J. Issaq, Timothy D. Veenstra, Thomas P. Conrads, , and Donna Felschow. The SELDI-TOF MS approach to proteomics: Protein profiling and biomarker identification. Biochemical and Biophysical Research Communications, 292:587–592, 2002. z
SELDI-TOF-MS zSurface Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry zUsed to profile protein markers from tissue or bodily fluids and thus identify biomarkers that can aid in diagnosis, prognosis or treatment. zApplication: psychiatric disease, renal function, cancer (pancreatic, prostate, ovarian, and breast)
SELDI-TOF-MS Components •
ProteinChip array –
•
Reader –
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Retain specific proteins from the sample Measures the molecular weights of the retained proteins and generates a trace showing the relative abundance vs. the molecular weights of these proteins
Software –
Identify differences in protein abundances between two samples
Source:http://www.rci.rutgers.edu/~layla/AnalMedChem511/pdf_files/RB_pdf/403featu re_issaq.pdf
Preparation •
Biological samples are processed via fractionation.
•
Fractionation: the process of splitting the original sample into subsamples which contain proteins that are more homogeneous
EAM: Energy Absorbing Molecule
Source:http://urology.jhu.edu/research/img1/proteomics13.jpg
Preprocessing of MS data zAlignment of the spectra zFiltering (Denoising) zBaseline subtraction zNormalization zPeak Detection zClustering of peaks zPeak quantification
SELDI-TOF-MS softwares •
ProteinChip Software 3.1
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SpecAlign
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Cromwell
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PROcess
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MassSpecWAvelet
PROcess package •
Process a single spectrum
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Process a set of spectra
Process a single spectrum •
Baseline subtraction
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Peak detection
Baseline subtraction zPurpose: To level off the elevated, non-constant baseline caused by the chemical noise in the EAM and by ion overload, thus, make different spectra compatible. zSolution: Using local regression to estimate the bottom of a spectrum and then subtracting that estimate from a spectrum zTwo approaches: Fitting local regression to: zThe points below a certain quantile zLocal minima: yields better results when estimating the baseline.
Baseline Subtraction
Baseline subtraction: algorithm zFor each spectrum, find local minima by segmenting the m/z range. zFit a local regression to local minima for each spectrum zSubtract the estimated baseline from each spectrum
### Load libraries library(survival) library(Icens) library(PROcess)
### Read in the raw spectrum fdat
