I think 4 levels should be plenty. I think maybe we should improve the message also to let the user know it looks in parent folders. 2 levels up is already a pretty crowded folder:
07/20/2019 04:53 PM <DIR> .
07/20/2019 04:53 PM <DIR> ..
03/11/2017 06:51 PM <DIR> B_D140314_SGSDSsample1_R01_MSG_T0
03/11/2017 06:51 PM <DIR> B_D140314_SGSDSsample1_R02_MSG_T0
03/11/2017 06:51 PM <DIR> B_D140314_SGSDSsample1_R03_MSG_T0
03/11/2017 06:51 PM <DIR> B_D140314_SGSDSsample2_R01_MSG_T0
03/11/2017 06:51 PM <DIR> B_D140314_SGSDSsample2_R02_MSG_T0
03/11/2017 06:51 PM <DIR> B_D140314_SGSDSsample2_R03_MSG_T0
03/11/2017 06:52 PM <DIR> B_D140314_SGSDSsample3_R01_MSG_T0
03/11/2017 06:52 PM <DIR> B_D140314_SGSDSsample3_R02_MSG_T0
03/11/2017 06:52 PM <DIR> B_D140314_SGSDSsample3_R03_MSG_T0
03/11/2017 06:52 PM <DIR> B_D140314_SGSDSsample4_R01_MSG_T0
03/11/2017 06:52 PM <DIR> B_D140314_SGSDSsample4_R02_MSG_T0
03/11/2017 06:52 PM <DIR> B_D140314_SGSDSsample4_R03_MSG_T0
03/11/2017 06:53 PM <DIR> B_D140314_SGSDSsample5_R01_MSG_T0
03/11/2017 06:53 PM <DIR> B_D140314_SGSDSsample5_R02_MSG_T0
03/11/2017 06:53 PM <DIR> B_D140314_SGSDSsample5_R03_MSG_T0
03/11/2017 06:53 PM <DIR> B_D140314_SGSDSsample6_R01_MSG_T0
03/11/2017 06:53 PM <DIR> B_D140314_SGSDSsample6_R02_MSG_T0
03/11/2017 06:53 PM <DIR> B_D140314_SGSDSsample6_R03_MSG_T0
03/11/2017 06:53 PM <DIR> B_D140314_SGSDSsample7_R01_MSG_T0
03/11/2017 06:54 PM <DIR> B_D140314_SGSDSsample7_R02_MSG_T0
03/11/2017 06:54 PM <DIR> B_D140314_SGSDSsample7_R03_MSG_T0
03/11/2017 06:54 PM <DIR> B_D140314_SGSDSsample8_R01_MSG_T0
03/11/2017 06:54 PM <DIR> B_D140314_SGSDSsample8_R02_MSG_T0
03/11/2017 06:54 PM <DIR> B_D140314_SGSDSsample8_R03_MSG_T0
03/11/2017 06:55 PM <DIR> combined
02/13/2015 11:50 AM 7,660,806 B_D140314_SGSDSsample1_R01_MSG_T0.index
02/13/2015 11:50 AM 7,673,646 B_D140314_SGSDSsample1_R02_MSG_T0.index
02/13/2015 11:50 AM 7,765,846 B_D140314_SGSDSsample1_R03_MSG_T0.index
02/13/2015 11:50 AM 7,639,746 B_D140314_SGSDSsample2_R01_MSG_T0.index
02/13/2015 11:50 AM 7,711,446 B_D140314_SGSDSsample2_R02_MSG_T0.index
02/13/2015 11:50 AM 7,751,266 B_D140314_SGSDSsample2_R03_MSG_T0.index
02/13/2015 11:51 AM 7,629,046 B_D140314_SGSDSsample3_R01_MSG_T0.index
02/13/2015 11:51 AM 7,712,626 B_D140314_SGSDSsample3_R02_MSG_T0.index
02/13/2015 11:51 AM 7,671,446 B_D140314_SGSDSsample3_R03_MSG_T0.index
02/13/2015 11:51 AM 7,701,666 B_D140314_SGSDSsample4_R01_MSG_T0.index
02/13/2015 11:51 AM 7,734,566 B_D140314_SGSDSsample4_R02_MSG_T0.index
02/13/2015 11:51 AM 7,713,946 B_D140314_SGSDSsample4_R03_MSG_T0.index
02/13/2015 11:52 AM 7,706,006 B_D140314_SGSDSsample5_R01_MSG_T0.index
02/13/2015 11:52 AM 7,745,626 B_D140314_SGSDSsample5_R02_MSG_T0.index
02/13/2015 11:52 AM 7,769,406 B_D140314_SGSDSsample5_R03_MSG_T0.index
02/13/2015 11:52 AM 7,706,146 B_D140314_SGSDSsample6_R01_MSG_T0.index
02/13/2015 11:52 AM 7,768,626 B_D140314_SGSDSsample6_R02_MSG_T0.index
02/13/2015 11:52 AM 7,723,726 B_D140314_SGSDSsample6_R03_MSG_T0.index
02/13/2015 11:52 AM 7,693,806 B_D140314_SGSDSsample7_R01_MSG_T0.index
02/13/2015 11:52 AM 7,765,646 B_D140314_SGSDSsample7_R02_MSG_T0.index
02/13/2015 11:52 AM 7,744,966 B_D140314_SGSDSsample7_R03_MSG_T0.index
02/13/2015 11:52 AM 7,762,226 B_D140314_SGSDSsample8_R01_MSG_T0.index
02/13/2015 11:52 AM 7,748,706 B_D140314_SGSDSsample8_R02_MSG_T0.index
02/13/2015 11:52 AM 7,716,286 B_D140314_SGSDSsample8_R03_MSG_T0.index
02/13/2015 11:50 AM 12,531 mqpar.xml
It is strange that this structure also appears to have _T0 as a suffix of all of the names. I wonder why that suffix appears to be stripped off in the Raw File field of the msms.txt. I had to rename all of the raw data files to get the library to build:
11/11/2014 01:00 AM 4,704,988 A_D141110_0uM-APAP_MnsMRM_R01.raw
11/11/2014 01:00 AM 4,705,270 A_D141110_0uM-APAP_MnsMRM_R02.raw
11/11/2014 01:00 AM 4,705,270 A_D141110_0uM-APAP_MnsMRM_R03.raw
11/11/2014 01:00 AM 4,705,270 A_D141110_3333uM-APAP_MnsMRM_R01.raw
11/11/2014 01:00 AM 4,704,988 A_D141110_3333uM-APAP_MnsMRM_R02.raw
11/11/2014 01:00 AM 4,704,988 A_D141110_3333uM-APAP_MnsMRM_R03.raw
10/24/2014 01:00 AM 871,557,166 B_D140314_SGSDSsample1_R01_MSG.raw
10/25/2014 01:00 AM 915,130,482 B_D140314_SGSDSsample1_R02_MSG.raw
10/25/2014 01:00 AM 892,220,522 B_D140314_SGSDSsample1_R03_MSG.raw
10/24/2014 01:00 AM 883,435,019 B_D140314_SGSDSsample2_R01_MSG.raw
10/25/2014 01:00 AM 899,057,884 B_D140314_SGSDSsample2_R02_MSG.raw
10/25/2014 01:00 AM 887,758,054 B_D140314_SGSDSsample2_R03_MSG.raw
10/25/2014 01:00 AM 895,456,567 B_D140314_SGSDSsample3_R01_MSG.raw
10/25/2014 01:00 AM 923,474,482 B_D140314_SGSDSsample3_R02_MSG.raw
10/25/2014 01:00 AM 900,043,464 B_D140314_SGSDSsample3_R03_MSG.raw
10/25/2014 01:00 AM 909,388,496 B_D140314_SGSDSsample4_R01_MSG.raw
10/25/2014 01:00 AM 926,623,154 B_D140314_SGSDSsample4_R02_MSG.raw
10/24/2014 01:00 AM 882,471,620 B_D140314_SGSDSsample4_R03_MSG.raw
10/24/2014 01:00 AM 878,463,077 B_D140314_SGSDSsample5_R01_MSG.raw
10/24/2014 01:00 AM 885,207,390 B_D140314_SGSDSsample5_R02_MSG.raw
10/25/2014 01:00 AM 892,749,324 B_D140314_SGSDSsample5_R03_MSG.raw
10/24/2014 01:00 AM 878,931,703 B_D140314_SGSDSsample6_R01_MSG.raw
10/25/2014 01:00 AM 898,930,076 B_D140314_SGSDSsample6_R02_MSG.raw
10/24/2014 01:00 AM 881,770,654 B_D140314_SGSDSsample6_R03_MSG.raw
10/25/2014 01:00 AM 893,247,106 B_D140314_SGSDSsample7_R01_MSG.raw
10/25/2014 01:00 AM 910,046,130 B_D140314_SGSDSsample7_R02_MSG.raw
10/24/2014 01:00 AM 857,501,892 B_D140314_SGSDSsample7_R03_MSG.raw
10/25/2014 01:00 AM 903,981,613 B_D140314_SGSDSsample8_R01_MSG.raw
10/25/2014 01:00 AM 905,201,293 B_D140314_SGSDSsample8_R02_MSG.raw
10/24/2014 01:00 AM 856,177,459 B_D140314_SGSDSsample8_R03_MSG.raw