DeMeanderize

Repairs MALDI experiments which were spotted line by line in a meandering pattern.

pot pot pot

Problem Description:

MALDI (Matrix-Assisted Laser Desorption/Ionization) spotting robots often apply samples to target plates in a "meandering" or "snake-like" pattern to optimize spotting efficiency. This means:

• Row 1 is spotted from left to right: spots 1, 2, 3, ..., N
• Row 2 is spotted from right to left: spots N+1, N+2, ..., 2N (but in reverse physical order!)
• Row 3 is spotted from left to right again: spots 2N+1, 2N+2, ..., 3N
• And so on...

When the mass spectrometer reads these spots in physical order (left to right for all rows), the spectra from alternating rows have incorrect retention time assignments, appearing in reverse chronological order compared to when they were spotted.

Solution:

DeMeanderize corrects this by:

1. Identifying MS1 spectra that belong to reversed rows
2. Recalculating their pseudo-retention times (RT) to reflect the actual spotting order
3. Sorting all spectra by their corrected RT values

Algorithm Details:

The tool processes spectra sequentially and assigns pseudo-RT values:

• For normal rows (first, third, fifth, etc.):

  RT = spectrum_number * RT_distance

• For reversed rows (second, fourth, sixth, etc.):

  RT = (row_start_number + (num_spots_per_row - position_in_row)) * RT_distance

The algorithm maintains:

• A counter tracking total MS1 spectra processed
• The position within the current row (0 to num_spots_per_row-1)
• A flag indicating whether the current row should be reversed

After processing num_spots_per_row MS1 spectra, the algorithm switches to the next row and toggles the reversal flag.

Parameters:

• num_spots_per_row: Number of spots in each row of the plate (default: 48)
• RT_distance: The pseudo-RT spacing between adjacent spots (default: 1.0)

Example:

For a plate with 4 spots per row and RT_distance=1.0:

Original physical order:  1  2  3  4  8  7  6  5  9 10 11 12
Spotting order:           1  2  3  4  5  6  7  8  9 10 11 12
Original RTs:             1  2  3  4  5  6  7  8  9 10 11 12
Corrected RTs:            1  2  3  4  8  7  6  5  9 10 11 12

After correction and sorting, spectra are ordered by actual spotting sequence.

The command line parameters of this tool are:

INI file documentation of this tool: