The Excel file containing the mass lists must follow some conventions.
The file consists of several sheets, each representing a lipid (molecule) class. If you want to analyze several lipid classes, just make several sheets. Second, there must be a header column. The header column must contain the following keywords, otherwise it won’t be accepted: Name, tR (min), at least one mass(…), and at least one element column. Except of the “Name” column, which must be the first column, the order of the columns does not matter for the Excel file. Detailed description of the example in the figure (columns from right to left):
| - | “Name”: The name of the analyte |
| - | “dbs”: This column is optional. If the analyte name contains double bonds in it, they should be entered in this column. The values of this column must be integer format. If the name of the analyte does not contain any double bonds, just remove this column. Generally, it is possible to enter the double bonds in the “Name” column directly; however, the sorting of the analytes in the results is improved if this column is used. |
| - | Element columns (“C”, ”H”, ”O”, “P”, “N”, “D”): In this column the elemental composition (chemical formula) of the analyte has to be entered. The values of this column must be in integer format. If there is a value in float format (e.g. the M column), the column will be ignored as elemental column (a warning at the beginning of the quantitation appears). A column is an elemental column if it contains just one or two characters, beginning in upper case and ending lower case (e.g. H, Na, He, P, etc.). If you require new elements, just add an additional column and enter the probable occurrences in nature in the elementconfig.xml file (see Configuration settings where to find this file). |
| - | Additional calculation columns (e.g. “M”, “MH+”): These columns are not read by the application, and are just a help for the user to calculate the masses. Do not mind that the comma in the float value is a “,” and not a “.”, the Excel I used for the screen shot is using the German notation. |
| - | Mass columns (“mass(…)”): A mass column contains the mass values to be quantified. There can be several mass columns because of different modifications/adducts. A mass column must contain the keyword “mass” followed by round brackets. Within the round brackets, there must be the keywords “name” and “form” followed by square brackets […]. In the square brackets after “name” the display name has to be entered; after form the chemical formula. The chemical formula of the modification/adduct must be in the notation $element_symbol$$element_amount$(e.g. H4). If no element amount is entered, it is assumed to be one (e.g. NH4=N1H4). If elements are lost by the modification enter a “-“ in front (e.g. –NH4 would correspond to a loss in ammonium). A space is interpreted as +, that means if you enter “-N H4” this would correspond to –N+H4. Additionally, the charge state can be entered by charge=$charge_state$. If this information is missing in the brackets, a charge state of 1 is assumed. |
| - | tR (min): This is the retention time column. The input of the retention time is optional. If it has not been entered, the whole chromatogram is searched for a peak (if the checkbox “Find molecules where retention time is unknown” is checked). |
Third, it is possible to enter a general start and stop retention time for a lipid class. The notation is “Start-RT: …” and “Stop-RT: …”. These cells can be anywhere before the row with the header row.