Questions about "*" in database and crash down when combining

[Qianjie Wang]

Hello Dear TopPIC team,

Greetings from Qianjie, one of the graduate students in Sun Lab at MSU.

I have two questions to ask and really appreciate if you could help with.

1. I am using the Arabidopsis database from TAIR as attached (https://michiganstate-my.sharepoint.com/:u:/g/personal/pklundqu_msu_edu/EQtz1V5WQdBNg2bHjquJ5bsBZJm5NK_kz_eTl0Hglty3uA?email=lsun%40chemistry.msu.edu&e=7DEM9v). So there are ~ 30 proteins with uncurtained amino acid "*". And there shows the errors I screenshotted.

My question: when we do the database searching, will it skip the "*" or will skip the sequence?

2. My second question is something that happened to me when I tried to combine the different files using the code on our high-performance computing system and it always crashed due to memory issues. Also, if I run thru the GUI software, it is frozen and no responding when it comes to the final combination step. Do you have any suggestions for that? 

Appreciate your help in building and maintaining the software. Hope to hear from you!

Best,

Qianjie

[liuxia...@gmail.com]

Hi, Qianjie, 

Thank you for using TopPIC. When protein sequences contain invalid amino acids in the fasta file, TopPIC will remove these invalid amino acids from the protein sequences and use the remaining sequences for proteoform identification. So the answer to your first question is that TopPIC will skip the "*", not the sequence. 

As for the second question, I assume that you encountered an error in TopDiff. Could you share with us the screenshot of TopDiff?

Best, 

Xiaowen

[Qianjie Wang]

Hello Dr. Liu,

Thank you for catching up and the explanation to question 1. 

Unfortunately, I haven't solved question #2 with multiple trial. So I am not using TopDiff, but MSConvert -> TopFD -> TopPIC as the manual suggested. So I have two same files with same operation, and I succeeded in one months ago. For the second file, I have failed from TopPIC_GUI.exe 1.4.0, and it crashed like the figure Stopped_working.jpg and I couldn't see the reason. 

So this happened before but if I repeated it, some time it worked but for this file, it keeps happening this time and crashing on similar position. So is there any suggestions?

Also, I have been doing this on our high performance computing where they offered the slurm.out file. I was stuck at this error like figure Slurm_out.jpg below while the administrative suggesting it could because of the memory issue but updating it to 800G didn't solve it. 

Then he suggested to update it into latest version #1..4.3 with a new virtual place to try. But this time I met another problem saying no Arabidopsis_decoy database even I put one decoy database into the folder. For your information, I also attached the sbatch file in the email.  I am not sure what happened because I included all file generated after TopFD as file.jpg suggested below. All the parameter I used in the 1.4.0 GUI.exe is same as the 1.4.3 HPC sbatch, with thread number equals to 4. I wonder if you could help with this database searching and really appreciate your caring and supporting for the software.

[wangqi50@dev-amd20-v100 20200813_chloroplast_0701_low]$ ls

07_01_Fraction_10_14_low_120min_10microscan_100ms_250ul_feature.xml

07_01_Fraction_10_14_low_120min_10microscan_100ms_250ul_file

07_01_Fraction_10_14_low_120min_10microscan_100ms_250ul_html

07_01_Fraction_10_14_low_120min_10microscan_100ms_250ul_ms1.feature

07_01_Fraction_10_14_low_120min_10microscan_100ms_250ul_ms2.feature

07_01_Fraction_10_14_low_120min_10microscan_100ms_250ul_ms2.msalign

07_01_Fraction_10_14_low_120min_10microscan_100ms_250ul.mzML

0701_fraction_10_14_low_200ul_feature.xml

0701_fraction_10_14_low_200ul_file

0701_fraction_10_14_low_200ul_html

0701_fraction_10_14_low_200ul_ms1.feature

0701_fraction_10_14_low_200ul_ms2.feature

0701_fraction_10_14_low_200ul_ms2.msalign

0701_fraction_10_14_low_200ul.mzML

07_01_Fraction_14_18_low_120min_10microscan_100ms_250ul_feature.xml

07_01_Fraction_14_18_low_120min_10microscan_100ms_250ul_file

07_01_Fraction_14_18_low_120min_10microscan_100ms_250ul_html

07_01_Fraction_14_18_low_120min_10microscan_100ms_250ul_ms1.feature

07_01_Fraction_14_18_low_120min_10microscan_100ms_250ul_ms2.feature

07_01_Fraction_14_18_low_120min_10microscan_100ms_250ul_ms2.msalign

07_01_Fraction_14_18_low_120min_10microscan_100ms_250ul.mzML

07_01_Fraction_18_20_low_120min_10microscan_100ms_200ul_feature.xml

07_01_Fraction_18_20_low_120min_10microscan_100ms_200ul_file

07_01_Fraction_18_20_low_120min_10microscan_100ms_200ul_html

07_01_Fraction_18_20_low_120min_10microscan_100ms_200ul_ms1.feature

07_01_Fraction_18_20_low_120min_10microscan_100ms_200ul_ms2.feature

07_01_Fraction_18_20_low_120min_10microscan_100ms_200ul_ms2.msalign

07_01_Fraction_18_20_low_120min_10microscan_100ms_200ul.mzML

07_01_Fraction_20_22_low_120min_10microscan_100ms_200ul_feature.xml

07_01_Fraction_20_22_low_120min_10microscan_100ms_200ul_file

07_01_Fraction_20_22_low_120min_10microscan_100ms_200ul_html

07_01_Fraction_20_22_low_120min_10microscan_100ms_200ul_ms1.feature

07_01_Fraction_20_22_low_120min_10microscan_100ms_200ul_ms2.feature

07_01_Fraction_20_22_low_120min_10microscan_100ms_200ul_ms2.msalign

07_01_Fraction_20_22_low_120min_10microscan_100ms_200ul.mzML

07_01_Fraction_22_24_low_120min_10microscan_100ms_200ul_feature.xml

07_01_Fraction_22_24_low_120min_10microscan_100ms_200ul_file

07_01_Fraction_22_24_low_120min_10microscan_100ms_200ul_html

07_01_Fraction_22_24_low_120min_10microscan_100ms_200ul_ms1.feature

07_01_Fraction_22_24_low_120min_10microscan_100ms_200ul_ms2.feature

07_01_Fraction_22_24_low_120min_10microscan_100ms_200ul_ms2.msalign

07_01_Fraction_22_24_low_120min_10microscan_100ms_200ul.mzML

07_01_Fraction_24_26_low_120min_10microscan_100ms_200ul_dilute_feature.xml

07_01_Fraction_24_26_low_120min_10microscan_100ms_200ul_dilute_file

07_01_Fraction_24_26_low_120min_10microscan_100ms_200ul_dilute_html

07_01_Fraction_24_26_low_120min_10microscan_100ms_200ul_dilute_ms1.feature

07_01_Fraction_24_26_low_120min_10microscan_100ms_200ul_dilute_ms2.feature

07_01_Fraction_24_26_low_120min_10microscan_100ms_200ul_dilute_ms2.msalign

07_01_Fraction_24_26_low_120min_10microscan_100ms_200ul_dilute.mzML

07_01_Fraction_26_30_low_120min_10microscan_100ms_dilute_feature.xml

07_01_Fraction_26_30_low_120min_10microscan_100ms_dilute_file

07_01_Fraction_26_30_low_120min_10microscan_100ms_dilute_html

07_01_Fraction_26_30_low_120min_10microscan_100ms_dilute_ms1.feature

07_01_Fraction_26_30_low_120min_10microscan_100ms_dilute_ms2.feature

07_01_Fraction_26_30_low_120min_10microscan_100ms_dilute_ms2.msalign

07_01_Fraction_26_30_low_120min_10microscan_100ms_dilute.mzML

07_01_Fraction_30_36_low_120min_10microscan_100ms_feature.xml

07_01_Fraction_30_36_low_120min_10microscan_100ms_file

07_01_Fraction_30_36_low_120min_10microscan_100ms_html

07_01_Fraction_30_36_low_120min_10microscan_100ms_ms1.feature

07_01_Fraction_30_36_low_120min_10microscan_100ms_ms2.feature

07_01_Fraction_30_36_low_120min_10microscan_100ms_ms2.msalign

07_01_Fraction_30_36_low_120min_10microscan_100ms.mzML

07_01_Fraction_36_end_low_120min_10microscan_100ms_dilute_feature.xml

07_01_Fraction_36_end_low_120min_10microscan_100ms_dilute_file

07_01_Fraction_36_end_low_120min_10microscan_100ms_dilute_html

07_01_Fraction_36_end_low_120min_10microscan_100ms_dilute_ms1.feature

07_01_Fraction_36_end_low_120min_10microscan_100ms_dilute_ms2.feature

07_01_Fraction_36_end_low_120min_10microscan_100ms_dilute_ms2.msalign

07_01_Fraction_36_end_low_120min_10microscan_100ms_dilute.mzML

Araport11_proteins.201606.fasta

modifications.txt

slurm-15884226.out

topdown_5.sbatch

 

[liuxia...@gmail.com]

Hi, Qianjie, 

Another user reported a similar problem about crashing at the step of outputting tables, and we have fixed the problem. Please use the latest version 1.4.7 and let us know if you find any problems. 

For the second question, if you run toppic to analyze multiple files simultaneously, please make sure that the MS files are in different folders and that there is a copy of the fasta file in each of the folders. Please let me know if there are any other problems with toppic. 

Best, 

Xiaowen