1. After selecting a group in the Transitions pane, the up and down arrow allow jumping by precursor ion. This is the fastest way to survey the data.
2. In the chromatogram pane, pushing the right mouse button while dragging adjusts the start and stop times for all ions in the group and recalculates the AUCs. This is the fastest way to curate a run. In a SILAC/AQUA experiment, the right button drag resets the start and stop for BOTH heavy and light precursor-product groups, recalculates the AUCs, and L/H ratios. Pushing the left mouse button while dragging zooms in on a region without changing the retention start and stop times.
3. Buttons can be operated by mouse or by pressing the Alt key and a second key to execute the command. The Alt key will cause underlining within the button to indicate which keys perform which commands.
4. The column widths in the elution data table are adjustable to permit easier visualization of tabular data on smaller monitors.
5. If a precursor product pair gives very poor signal and MRMer cannot generate a curve, it is rejected and the background in the chromatogram pane is set to light red.
6. In SILAC/AQUA runs, the light and heavy pairs are indicated by the L or H in the chromatogram window.
7. The timing button adds the letter "T" in the comment column for the entry reminding the operator that the scheduling might be off and that this transition group needs scrutiny.
8. The dwell button adds the letter "D" in the comment column to remind the operator that the dwell time should be lengthened (for low intensity transitions) or shortened (for very intense transitions).
9. MRMer can use a lot of memory when it is analyzing large mzXML files. The example .bat files provided with the distribution request sufficient memory on the java command line. The MRMer.bat file requests 600 megabytes, which is enough for most purposes. However, if you are analyzing a particularly large mzXML file, you may want to change the java command line option -Xmx600m to something like --Xmx1G. (1 gigabyte). If the memory you request is too small, you may see an error message like: "out of heap space" -- or MRMer may slow down to a useless speed. If you request more memory than you have available, you may see an error like "cannot create virtual machine."
10. Whenever MRMer can discover elution curves you will see a red triangle on top of the chromatogram. This triangle shows the value of the data-column "Mid-Time" and is designed to indicate the midpoint of the elution curve. You can change the position the mid-time marker by hand: click the middle mouse button (or wheel) over the X (time) position where you would prefer to see it.
11. The columns in the Elution Data table are interchangeable. You can move a column to a new position by positioning the mouse on the gray title bar and dragging the column to the desired position. This can be particularly useful if you have limited screen space.
12. Current version of MRMer (0.97_01) only runs under Java 1.6.

View an image of MRMer with precursor chromatograms, here

Structure of a Transition Definition File

Transition definition files provide information to MRMer over and above the information provided in the mzXML file. They are particularly useful in SILAC and AQUA analyses.

A transition definition file is placed in the same directory as its associated mzXML file. It has the same base name as the mzXML file with the extension: ".transition.tsv". It looks like this:

Line 1:   Transition definition file<TAB>Version 0.1
Line 2:   <Name of the mzXML (name and extension; no path)>
Line 3:   <Comment. Any text you like. It will appear on the top of the MRMer screen>
Lines 4 onward   Five tab-separated fields:

1. <Precursor Peptide><TAB>
2. <Precursor M/Z><TAB>
3. <Product M/Z><TAB>
4. <L or H for 'Low' or 'High' label><TAB>
5. <Numeric code linking L or H pairs; Both heavy and light reaction pairs get the same code>

The first three lines are required, although the second two may be blank. Any field may be blank on the remaining data lines. Trailing blank fields may be omitted. The lines in the transition definition file are matched to transitions inferred by MRMer by matching the precursor and product M/Z values to the inferred precursor and producted M/Z values within a tolerance of precursor_tolerance and product_tolerance, respectively. If no match is found, MRMer ignores the information for that line in the transition definition file.

Here is an example:

Transition definition file	Version: 0.1
QP20071218_SILAC_1_4_08.mzXML
154 SILAC pairs 1:4
TANDVLTIR	501.778	        830.474	        L	1	
TANDVLTIR	506.7821345	840.482269	H	1	
YHIEEEGSR	560.2523	819.3851	L	7	
YHIEEEGSR	565.2564345	829.393369	H	7	
YHIEEEGSR	560.2523	706.3009	L	8	
YHIEEEGSR	565.2564345	716.309169	H	8	
LLSEEALPAIR	606.3526	640.4174	L	9	
LLSEEALPAIR	611.3567345	650.425669	H	9	
LLSEEALPAIR	606.3526	569.3754	L	10	
LLSEEALPAIR	611.3567345	579.383669	H	10	
LLSEEALPAIR	606.3526	769.4587	L	11	
LLSEEALPAIR	611.3567345	779.466969	H	11