ISCB2017 - Workshop for Proteomics Data Analysis and Bioinformatics (p2364 ) This R package contains data and vignette files for
a Pigeon Pea (Cajanus cajan) project from
a Indo-Swiss Collaboration in Biotechnology (ISCB)
training course on proteome informatics given
from January 21th to January 25th 2017 at the
National Research Centre on Plant Biotechnology (NRCPB) in New Delhi-110012 by
JG ,
WEW , and
CP .
Morning Session: Responsible SE -> Ingrid & Urs
Afternoon Session: Responsible PrXIT -> Jonas
Day 2 (Protein Identifications)
Module Number
Theoretical Part
Hands-on Module
Duration
Main responsible Person
1
Outline for this week
break
0.5 h
jg
2
The FGCZ in Zurich
browse FGCZ page
0.5 h
jg
3
Mass spectrometry (and protein analytics)
browse around for milestones in MS, form groups, introduce yourself and your task
1 h
jg
4
Getting ready for hands-on sessions
Install MQ, do git co, commits, get R packages
1 h
CP
5
PSM identification with protViz get fasta, R (seqinR), R (digest), theoretical considerations about search space, different DBs, uniqueness of peptides. 2.5h
CP
6
Protein identification VALIDATION with target-decoy strategy
FDR 2h
WEW
7
Start your own MQ
run it on your PC
1h
jg
8
Conclusion of day 1
Q & A
1h
all
Day 3 (Protein Quantification)
Module Number
Theoretical Part
Hands-on Module
Duration
Main responsible Person
1
Repetition of Day 1
Q & A
0.5 h
all
2
About Plots
coffee break
0.5 h
JG
3
Protein, Peptide, Mass-spec view and LFQ
hands-on LFQ 3h
JG/CP
4
Experimental design in quant experiments
Looking at annotation of samples in Bfabric
1h
jg
5
Two group analysis for Yeast, grown on different nutrient sources
Analysing 2 groups in R-quantable
2h
WEW
6 & 7
Principle of ORA and Webtools for model organisms
Webgestalt, StringDB, YeastCyc w YEAST results
2h
cpNjg
8
Conclusion of day 2
Q & A
1h
jg
Day 5 -> Look at Pigeon Pea and Wrap up of the whole course -> identify room for improvements ;)
Module Number
Theoretical Part
Hands-on Module
Duration
Main responsible Person
1
Repetition of Day 3
Q & A
0.5 h
all
2
fun with
R, CRAN & Bioconductor
1.5 h
CP/WEW
3
blast
0.3 h
CP
4
Look at the Pigeon Pea project
Make use of what we learnt in the pigeon pea project
3h
all
5
Wrap up of the course
Course Evaluation
1h
all
additionally if we have too much time ;)
Quantitative proteomics strategies (an overview) | break | 1h | jg | Combo-course day4 (NSK) (show 12)
Label-free quantification | MQ: txt-tables | 1h | jg | Combo-course day4 (partI) (show 13)
YeastData: RNASeq vs PrX: Number crunch | Shiny-app | jg | 1h
own laptop (Windows or Mac/Linux w Virtual Box and Windows instance)
equiped with: Editor (vi, nano, ..), R., RStudio, git
some free space (20gigs at least)
http://fgcz-bfabric.uzh.ch/bfabric/userlab/show-project.html?projectId=2364
Publications to study (upfront) install the ISCB2017 R package install.packages('devtools')
library(devtools)
install_git('https://github.com/fgcz/ISCB2017', build_vignettes = TRUE, quiet = FALSE)
build the ISCB2017 R package # get an overview
library(ISCB)
vignette(package="ISCB2017")
vignette('peakplot')
vignette('fdr')
vignette('lfq')