ERROR: Unexpected cycle shape. Will only retain first frame group

[ht-lau]

Hi,

I ran into the error, unexpected cycle shape. I wonder if it is because of my instrument method. My instrument is the TimsTOF pro2, and the following is the diaPASEF cycle. Note that there is an extra MS1 cycle.

MS Type,Cycle Id,Start IM [1/K0],End IM [1/K0],Start Mass [m/z],End Mass [m/z],CE [eV]

MS1,0,-,-,-,-,- MS1,6,-,-,-,-,- PASEF,1,0.6,0.88,250,445.54647,- PASEF,2,0.6,0.905,444.54647,495.256462,- PASEF,3,0.6,0.925,494.256462,529.802078,- PASEF,4,0.6,0.945,528.802078,559.286462,- PASEF,5,0.6,0.965,558.286462,584.80554,- PASEF,7,0.6,0.99,583.80554,609.82119,- PASEF,8,0.6,1.01,608.82119,634.338758,- PASEF,9,0.6,1.04,633.338758,659.809144,- PASEF,10,0.6,1.06,658.809144,684.637416,- PASEF,11,0.6,1.12,683.637416,710.29279,- PASEF,1,0.88,1.6,709.29279,736.406824,- PASEF,2,0.905,1.6,735.406824,764.869666,- PASEF,3,0.925,1.6,763.869666,794.428074,- PASEF,4,0.945,1.6,793.428074,826.857108,- PASEF,5,0.965,1.6,825.857108,862.89685,- PASEF,7,0.99,1.6,861.89685,904.9257,- PASEF,8,1.01,1.6,903.9257,956.563184,- PASEF,9,1.04,1.6,955.563184,1025.994042,- PASEF,10,1.06,1.6,1024.994042,1128.06233,- PASEF,11,1.12,1.6,1127.06233,1800,-

Following is part of the log (v1.6.2, GUI)

0:03:56.267669 PROGRESS: Starting Search Workflows 0:03:56.267669 PROGRESS: Loading raw file 1/14: 20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316 0:03:56.267669 INFO: Creating parent folder for workflows at E:\MSdata\20240423_prmInter7_rep4_intra_2columns\out_alphaDIA.progress 0:03:56.267669 INFO: Creating workflow folder for 20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316 at E:\MSdata\20240423_prmInter7_rep4_intra_2columns\out_alphaDIA.progress\20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316 0:03:56.267669 INFO: Importing data from E:\MSdata\20240423_prmInter7_rep4_intra_2columns\raw_DIA\20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316.d 0:03:56.267669 INFO: Using .d import for E:\MSdata\20240423_prmInter7_rep4_intra_2columns\raw_DIA\20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316.d 0:03:56.267669 INFO: Reading frame metadata for E:\MSdata\20240423_prmInter7_rep4_intra_2columns\raw_DIA\20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316.d 0:03:57.325609 INFO: Reading 19,710 frames with 1,221,717,704 detector events for E:\MSdata\20240423_prmInter7_rep4_intra_2columns\raw_DIA\20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316.d

0%| | 0/19710 [00:00<?, ?it/s] 0%| | 1/19710 [00:01<6:26:50, 1.18s/it] 1%| | 130/19710 [00:01<02:19, 140.27it/s] 3%|2 | 574/19710 [00:01<00:26, 715.62it/s] 6%|5 | 1102/19710 [00:01<00:12, 1446.41it/s] 8%|8 | 1631/19710 [00:01<00:08, 2161.50it/s] 11%|#1 | 2212/19710 [00:01<00:06, 2856.71it/s] 14%|#3 | 2664/19710 [00:01<00:06, 2651.39it/s] 15%|#5 | 3044/19710 [00:02<00:09, 1810.63it/s] 17%|#6 | 3334/19710 [00:02<00:10, 1573.20it/s] 18%|#8 | 3568/19710 [00:02<00:10, 1547.83it/s] 19%|#9 | 3775/19710 [00:02<00:10, 1537.38it/s] 20%|## | 3965/19710 [00:02<00:10, 1492.79it/s] 21%|## | 4138/19710 [00:03<00:10, 1464.65it/s] 22%|##1 | 4300/19710 [00:03<00:10, 1443.73it/s] 23%|##2 | 4455/19710 [00:03<00:10, 1466.31it/s] 23%|##3 | 4610/19710 [00:03<00:10, 1447.76it/s] 24%|##4 | 4761/19710 [00:03<00:10, 1387.16it/s] 25%|##4 | 4904/19710 [0:04:14.975387 INFO: Indexing E:\MSdata\20240423_prmInter7_rep4_intra_2columns\raw_DIA\20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316.d... 0:04:15.225177 INFO: Opening handle for E:\MSdata\20240423_prmInter7_rep4_intra_2columns\raw_DIA\20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316.d 0:04:15.241385 INFO: Fetching mobility values from E:\MSdata\20240423_prmInter7_rep4_intra_2columns\raw_DIA\20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316.d 0:04:15.241385 INFO: Closing handle for E:\MSdata\20240423_prmInter7_rep4_intra_2columns\raw_DIA\20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316.d 0:04:15.241385 INFO: Opening handle for E:\MSdata\20240423_prmInter7_rep4_intra_2columns\raw_DIA\20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316.d 0:04:15.281232 INFO: Fetching mz values from E:\MSdata\20240423_prmInter7_rep4_intra_2columns\raw_DIA\20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316.d 0:04:15.298119 INFO: Closing handle for E:\MSdata\20240423_prmInter7_rep4_intra_2columns\raw_DIA\20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316.d 0:04:15.302325 INFO: Indexing quadrupole dimension 0:04:15.868764 ERROR: Unexpected cycle shape. Will only retain first frame group 0:04:15.869275 ERROR: Search for 20240423_prmInter7_rep4_intra_0d5load_150ng_1_1_5316 failed with error Unexpected cycle shape. Will only retain first frame group Traceback (most recent call last): File "alphadia\planning.py", line 313, in run workflow.load(dia_path, speclib) File "alphadia\workflow\peptidecentric.py", line 122, in load super().load( File "alphadia\workflow\base.py", line 80, in load self._dia_data = self._get_dia_data_object(dia_data_path) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "alphadia\workflow\base.py", line 181, in _get_dia_data_object dia_data = bruker.TimsTOFTranspose( ^^^^^^^^^^^^^^^^^^^^^^^^ File "alphadia\data\bruker.py", line 70, in init raise ValueError( ValueError: Unexpected cycle shape. Will only retain first frame group 0:04:15.873912 INFO: Traceback (most recent call last): File "alphadia\cli.py", line 341, in run plan.run() File "alphadia\planning.py", line 358, in run raise e File "alphadia\planning.py", line 313, in run workflow.load(dia_path, speclib) File "alphadia\workflow\peptidecentric.py", line 122, in load super().load( File "alphadia\workflow\base.py", line 80, in load self._dia_data = self._get_dia_data_object(dia_data_path) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "alphadia\workflow\base.py", line 181, in _get_dia_data_object dia_data = bruker.TimsTOFTranspose( ^^^^^^^^^^^^^^^^^^^^^^^^ File "alphadia\data\bruker.py", line 70, in init raise ValueError( ValueError: Unexpected cycle shape. Will only retain first frame group

0:04:15.873912 ERROR: Unexpected cycle shape. Will only retain first frame group

Thank you in advance, HT

[GeorgWa]

Hi, we haven't processed diaPASEF data with repeated scans yet. Do you have a file and a small, matching library you can share?

[ht-lau]

I don’t have one that I can share. But I can run a HeLa lysate using this method. Will that work?

[GeorgWa]

This would be great! I also have a library for hela.

[ht-lau]

Georg, is there a place that I can upload it? Thanks

[GeorgWa]

Thanks! You should be able to upload it here: https://datashare.biochem.mpg.de/s/UFCrZBADX9JB22l

[ht-lau]

Uploaded. Thanks