R: fetuinLFQ - A data set for evaluation of relative and...

fetuinLFQ {protViz} | R Documentation

## fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods.

### Description

This data set contains the read-out abundance for three different methods (APEX, emPAI, T3PQ) for seven proteins from a complex yeast background (abundance levels unchanged) and the Fetuin that was spiked into the extracts in concentrations ranging from 20fmol to 300fmol on column (in triplicates).

Samples were analyzed on a LTQ-FTICR Ultra mass spectrometer (Thermo Fischer Scientific, Bremen, Germany) coupled to an Eksigent-Nano-HPLC system (Eksigent Technologies, Dublin (CA), USA).

The data can be derived out of the mzXML files:

1 186240760 2008-12-11 20080816_01_fetuin.mzXML

2 179013841 2008-12-11 20080816_02_fetuin_0.mzXML

3 178692924 2008-12-11 20080816_03_fetuin_0.mzXML

4 178608302 2008-12-11 20080816_04_fetuin_0.mzXML

5 180995463 2008-12-11 20080816_05_fetuin_20.mzXML

6 175934898 2008-12-11 20080816_06_fetuin_20.mzXML

7 178364454 2008-12-11 20080816_07_fetuin_20.mzXML

8 184376874 2008-12-11 20080816_08_fetuin_40.mzXML

9 187205031 2008-12-11 20080816_09_fetuin_40.mzXML

10 185646382 2008-12-11 20080816_10_fetuin_40.mzXML

11 183498944 2008-12-11 20080816_11_fetuin_60.mzXML

12 184752098 2008-12-11 20080816_12_fetuin_60.mzXML

13 186243524 2008-12-11 20080816_13_fetuin_60.mzXML

14 187794055 2008-12-11 20080816_14_fetuin_80.mzXML

15 183463368 2008-12-11 20080816_15_fetuin_80.mzXML

16 186331090 2008-12-11 20080816_16_fetuin_80.mzXML

17 188027950 2008-12-11 20080816_17_fetuin_100.mzXML

18 186881098 2008-12-11 20080816_18_fetuin_100.mzXML

19 187219923 2008-12-11 20080816_19_fetuin_100.mzXML

20 187157009 2008-12-11 20080816_20_fetuin_120.mzXML

21 190008885 2008-12-11 20080816_21_fetuin_120.mzXML

22 184226648 2008-12-11 20080816_22_fetuin_120.mzXML

23 190681343 2008-12-11 20080816_23_fetuin_160.mzXML

24 194653066 2008-12-11 20080816_24_fetuin_160.mzXML

25 191045349 2008-12-11 20080816_25_fetuin_160.mzXML

26 184869491 2008-12-11 20080816_26_fetuin_200.mzXML

27 185490782 2008-12-11 20080816_27_fetuin_200.mzXML

28 185635558 2008-12-11 20080816_28_fetuin_200.mzXML

29 187743192 2008-12-11 20080816_29_fetuin_300.mzXML

30 190613235 2008-12-11 20080816_30_fetuin_300.mzXML

31 189570723 2008-12-11 20080816_31_fetuin_300.mzXML

32 226404551 2008-12-11 20080819_32_fetuin.mzXML

contained in a 3GBytes compressed tar ball http://fgcz-data.uzh.ch/public/fqms.tgz.

The t3pq data can be derived using the code from http://fqms.svn.sourceforge.net/

### Format

A data set with approx. 600 rows and four variables, 4KBytes file size, derived out of 32 single LC-MS runs, 5GBytes size, of a protein mixture.

### Author(s)

Christian Panse 2009,2010

### References

http://www.ncbi.nlm.nih.gov/pubmed/20576481

### Examples

    library(lattice)
    data(fetuinLFQ)

    cv<-1-1:7/10
    t<-trellis.par.get("strip.background")
    t$col<-(rgb(cv,cv,cv))
    trellis.par.set("strip.background",t)

    my.xlab="Fetuin concentration spiked into experiment [fmol]"
    my.ylab<-"Abundance"

    xyplot(abundance~conc|prot*method,
        data=fetuinLFQ$apex,
        groups=prot,
        aspect=1,
        panel = function(x, y, subscripts, groups) {
            if (groups[subscripts][1] == "Fetuin")  {
                panel.fill(col="#ffcccc")
            }
                    panel.grid(h=-1,v=-1)
                    panel.xyplot(x, y)
                    panel.loess(x,y, span=1)
                },
        xlab=my.xlab,
        ylab=my.ylab
    )

    xyplot(abundance~conc|prot*method,
        data=fetuinLFQ$empai,
        groups=prot,
        aspect=1,
        panel = function(x, y, subscripts, groups) {
            if (groups[subscripts][1] == "Fetuin")  {
                panel.fill(col="#ffcccc")
            }
                    panel.grid(h=-1,v=-1)
                    panel.xyplot(x, y)
                    panel.loess(x,y, span=1)
                },
        xlab=my.xlab,
        ylab=my.ylab
    )

    xyplot(abundance~conc|prot*method,
        data=fetuinLFQ$t3pq,
        groups=prot,
        aspect=1,
        panel = function(x, y, subscripts, groups) {
            if (groups[subscripts][1] == "Fetuin")  {
                panel.fill(col="#ffcccc")
            }
                    panel.grid(h=-1,v=-1)
                    panel.xyplot(x, y)
                    panel.loess(x,y, span=1)
            if (groups[subscripts][1] == "Fetuin")  {
                panel.text(min(fetuinLFQ$t3pq$conc),
                    max(fetuinLFQ$t3pq$abundance),
                    paste("R-squared:",
                    round(summary(lm(x~y))$r.squared,2)),
                    cex=0.75,
                    pos=4)
            }
                },
        xlab=my.xlab,
        ylab=my.ylab
    )

[Package protViz version 0.2.45 Index]