The conversion breaks when it asks the vendor API to parse this looooooooooooooooooooooooong filter:
+ c NSI SRM ms2 863.468 [413.187-413.189, 413.187-413.189, 413.197-413.199, 413.197-413.199, 413.207-413.209, 413.207-413.209, 413.217-413.219, 413.217-413.219, 413.227-413.229, 413.227-413.229, 413.237-413.239, 413.237-413.239, 413.247-413.249, 413.247-413.249, 413.257-413.259, 413.257-413.259, 413.267-413.269, 413.267-413.269, 413.277-413.279, 413.277-413.279, 413.287-413.289, 413.287-413.289, 938.467-938.469, 938.467-938.469, 938.477-938.479, 938.477-938.479, 938.487-938.489, 938.487-938.489, 938.497-938.499, 938.497-938.499, 938.507-938.509, 938.507-938.509, 938.517-938.519, 938.517-938.519, 938.527-938.529, 938.527-938.529, 938.537-938.539, 938.537-938.539, 938.547-938.549, 938.547-938.549, 938.557-938.559, 938.557-938.559, 938.567-938.569, 938.567-938.569, 1067.510-1067.512, 1067.510-1067.512, 1067.520-1067.522, 1067.520-1067.522, 1067.530-1067.532, 1067.530-1067.532, 1067.540-1067.542, 1067.540-1067.542, 1067.550-1067.552, 1067.550-1067.552, 1067.560-1067.562, 1067.560-1067.562, 1067.570-1067.572, 1067.570-1067.572, 1067.580-1067.582, 1067.580-1067.582, 1067.590-1067.592, 1067.590-1067.592, 1067.600-1067.602, 1067.600-1067.602, 1067.610-1067.612, 1067.610-1067.612, 1180.594-1180.596, 1180.594-1180.596, 1180.604-1180.606, 1180.604-1180.606, 1180.614-1180.616, 1180.614-1180.616, 1180.624-1180.626, 1180.624-1180.626, 1180.634-1180.636, 1180.634-1180.636, 1180.644-1180.646, 1180.644-1180.646, 1180.654-1180.656, 1180.654-1180.656, 1180.664-1180.666, 1180.664-1180.666, 1180.674-1180.676, 1180.674-1180.676, 1180.684-1180.686, 1180.684-1180.686, 1180.694-1180.696, 1180.694-1180.696, 1295.621-1295.623, 1295.621-1295.623, 1295.631-1295.633, 1295.631-1295.633, 1295.641-1295.643, 1295.641-1295.643, 1295.651-1295.653, 1295.651-1295.653, 1295.661-1295.663, 1295.661-1295.663, 1295.671-1295.673, 1295.671-1295.673, 1295.681-1295.683, 1295.681-1295.683, 1295.691-1295.693, 1295.691-1295.693, 1295.701-1295.703, 1295.701-1295.703, 1295.711-1295.713, 1295.711-1295.713, 1295.721-1295.723, 1295.721-1295.723, 1394.689-1394.691, 1394.689-1394.691, 1394.699-1394.701, 1394.699-1394.701, 1394.709-1394.711, 1394.709-1394.711, 1394.719-1394.721, 1394.719-1394.721, 1394.729-1394.731, 1394.729-1394.731, 1394.739-1394.741, 1394.739-1394.741, 1394.749-1394.751, 1394.749-1394.751, 1394.759-1394.761, 1394.759-1394.761, 1394.769-1394.771, 1394.769-1394.771, 1394.779-1394.781, 1394.779-1394.781, 1394.789-1394.791, 1394.789-1394.791]
What is up with that filter? I did some testing and it's not the duplicate Q3 ranges (each one is represented twice) causing the failure. It seems to be the overall length of the filter. Why is every Q3 range duplicated? Without the duplication, the filter parser works.
The conversion actually also works with the old 32-bit MSFileReader API, just not with the new 64-bit RawFileReader one. This is not something we could easily fix in ProteoWizard. Brendan, do you want me to add some deduplication when filters exceed a certain length, or wait for Thermo to say whether they'll fix this limitation?