**IAMA documentation**

Data handler for MALDI mass
spectrometry dilution experiments.

**-HOW TO- GUIDE**

1.*Data source definition:*

1a. Browse and select
folders which contain a) MS intensity tables (for .xls* files: rows are m/z peak
IDs, columns are intensities with sample IDs as headers; or for .txt files:
each row contains sample data with embedded intensities); b) lookup tables
(sample definition tables with sample IDs in rows and associated information
(nested local IDs, file infos, etc.) in columns either as .xls*, .txt, or .log
files); c) m/z peak tables with peak IDs in rows and associated information in
columns. Select 'Cancel' to set to 'none'. Select 'use headers' if multiple
files in the folder might not have the same order of columns.

OR

1b. Paste MS intensity table
in sheet 1 and sample lookup table in sheet 2. m/z data will be automatically
added to the final output table if a m/z reference file has been selected.

The software will use either
1a or 1b depending on whether folders have been selected or not.

2*. Define data layout:*

2a. Enter the row numbers of
the global sample IDs and the start of the intensity data in the MS intensity
table(s) (source data). These have to contain m/z peak IDs as first column!

2b. Enter the column numbers
of the location of the same global sample IDs and the nested sub-ID (GlasgowID)
in the lookup table(s).

2c. Define the structure of
the nested sub-ID (

2d. Select 'acid' tag if you
wish to extract this tag from your nested sub-ID.

2e. Enter the value of the
normalisation factor (100 will render your intensity to percentages).

*Data manipulation:*

3. Calculate the sum of
intensities per sample: adds up all intensities per sample and reports the
number of peaks with intensity values (i.e. values above zero) per sample.

4. Take Glasgow ID apart:
will extract information such as dilutions and localised sample IDs from the
nested sub-ID.

5. Remove zeros in source
data: removes null values in the intensity tables. This has no impact on any
functions in the software (aesthetics only).

6. Normalise source data:
tallies the intensities by sample (column) and divides each value by the sum
total. Generates new table.

7. Merge by: select if and
how you wish to merge the source data. Generates new table.

8. Average data after merge:
select if you want to average the data after the merging operation. This will
omit null values. Choose to merge it on a new worksheet or merge it directly or
leave the data side-by-side (using '|' as a data separator). Generates new
table.

9. Minimum number of
replicates: define how many replicates you accept as a valid peak (lower
boundary). If this number is not reached (i.e. the peak was not observed with
the minimal number defined), then the intensity of this peak will be set to
zero or omitted. Enter '0' if you accept all peaks.

10. Maximum number of
replicates: define how many replicates you accept as a valid peak (higher
boundary). If there are more valid measurements for a specific peak, then the
software will either calculate the average and drop the one(s) furthest away
until the number of intensities reaches the value entered, or (if this number
specified is preceeded with a minus sign) drops the lowest values until the
number of intensities matches the specified value (without the minus sign).

11. Include number of
replicates when averaging: adds the number of replicates with observed
intensities after the averaged intensity in brackets.

12. Normalise after merging
and averaging: tallies the intensities by sample (column) and divides each
value by the sum total. Generates new table.

13. Sort data: select from
the drop-down list how you want the data to be sorted. Generates new table.

14. Regression analysis:
Select if you want to do regression analysis. This requires that the source
data has been merged. Generates new table.

15. Use data: applies only
to data which has not already been averaged. Either average it or use every
single datapoint for curve fitting.

16. Transform data: choose
to use the dilution data as is, or transform it to square root (brings the data
together) or quadratic (expands the data). The final output will be adjusted
accordingly (un-transformed).

17. Curve fitting: Choose
between linear, exponential or polynomial (n=2) curve fitting.

18. Drop outliers: Define
how many dilutions can be removed per m/z peak (applies only to valid
measurements). This is done by linear regression analysis, followed by
determination and removal of the outlier, and re-analysis by linear regression.
It will repeat this step until either the number stated is reached, or the
datapoint threshold value is reached.

19. Datapoint threshold:
Define the number of minimal dilution data points per m/z peak. If this number
is not reached for a m/z peak then the intensity will be set to null.

20. Intensity output: Select
whether the reported output intensity value should be calculated for a dilution
of 1 by either following the calculated regression curve, or calculating the
average of the valid dilution values (after removal of outliers if selected), calculating
the associated intensity based on the regression curve, and reporting the ratio
of this intensity value and the average dilution value.

21. Dilution factor: the
output will be calculated based on the defined dilution factor for all values.

22. Normalise after
regression analysis: tallies the intensities by sample (column) and divides
each value by the sum total.

23. Parameter output to
report: Select which parameters the software should include in the output (this
will be placed in the column next to the data output column).

23a. Number of dilutions:
number of merged dilutions with data (after data point adjustments).

23b. N(sample depth): total
number of datapoints used in calculation.

23c. R-square: the R-square
value (coefficient of determination).

23d. average dilution: the
average of all dilution-values used for the calculation (after data point
adjustment).

23e. average intensity: the
intensity value at the average dilution point.

23f. standard error
intensity: the standard error of the intensity after calculation.

23g. slope: the slope of
aligned curve.

23h. offset: the offset of
the aligned curve.

23i. F-statistic: F-observed
value. Determines whether the observed relationship between the dependent and
independent variables occurs by chance.

23j. dF: degree of freedom.

23k. F distribution: F
probability distribution.

23l. all: selects all output
options.

24. Select either 'Cancel'
to quit or 'Do it' to proceed. A summary window will pop-up where you can
review your settings and either go back to adjust the settings or continue to
do the data manipulations.

Source code is available
upon request by sending us
an email.