Zero proteins selected

[Sjan1]

Using sample data tmt-report therein, I managed to get config file. When executing tpprNormOneDTPP, no proteins are selected due to fold change filter settings. Here is a copy of console of the last command:

FragPipeTPP::tpprNormOneDTPP(configpath,FPpath)
Importing data...

Replacing config table column 'Replicate' by corresponding columns starting with suffix 'Comparison'.

Comparisons will be performed between the following experiments:
Treatment_1_vs_Vehicle_1
Treatment_2_vs_Vehicle_2

The following valid label columns were detected:
126, 127L, 127H, 128L, 128H, 129L, 129H, 130L, 130H, 131L.

Importing TR dataset: Treatment_1
Removing duplicate identifiers using quality column 'qupm'...
4 out of 4 rows kept for further analysis.
-> Treatment_1 contains 4 proteins.
-> 3 out of 4 proteins (75%) suitable for curve fit (criterion: > 2 valid fold changes per protein).

Importing TR dataset: Treatment_2
Removing duplicate identifiers using quality column 'qupm'...
4 out of 4 rows kept for further analysis.
-> Treatment_2 contains 4 proteins.
-> 3 out of 4 proteins (75%) suitable for curve fit (criterion: > 2 valid fold changes per protein).

Importing TR dataset: Vehicle_1
Removing duplicate identifiers using quality column 'qupm'...
4 out of 4 rows kept for further analysis.
-> Vehicle_1 contains 4 proteins.
-> 4 out of 4 proteins (100%) suitable for curve fit (criterion: > 2 valid fold changes per protein).

Importing TR dataset: Vehicle_2
Removing duplicate identifiers using quality column 'qupm'...
4 out of 4 rows kept for further analysis.
-> Vehicle_2 contains 4 proteins.
-> 3 out of 4 proteins (75%) suitable for curve fit (criterion: > 2 valid fold changes per protein).

Creating normalization set:
1. Filtering by non fold change columns:
Filtering by annotation column(s) 'qssm' in treatment group: Treatment_1
Column qssm between 4 and Inf-> 3 out of 4 proteins passed.

3 out of 4 proteins passed in total.

Filtering by annotation column(s) 'qssm' in treatment group: Treatment_2
Column qssm between 4 and Inf-> 3 out of 4 proteins passed.

3 out of 4 proteins passed in total.

Filtering by annotation column(s) 'qssm' in treatment group: Vehicle_1
Column qssm between 4 and Inf-> 3 out of 4 proteins passed.

3 out of 4 proteins passed in total.

Filtering by annotation column(s) 'qssm' in treatment group: Vehicle_2
Column qssm between 4 and Inf-> 3 out of 4 proteins passed.

3 out of 4 proteins passed in total.

2. Find jointP:

Detecting intersect between treatment groups (jointP).
-> JointP contains 3 proteins.

3. Filtering fold changes:

Filtering fold changes in treatment group: Treatment_1
Column 7 between 0.4 and 0.6 -> 0 out of 3 proteins passed
Column 9 between 0 and 0.3 -> 3 out of 3 proteins passed
Column 10 between 0 and 0.2 -> 3 out of 3 proteins passed
0 out of 3 proteins passed in total.

Filtering fold changes in treatment group: Treatment_2
Column 7 between 0.4 and 0.6 -> 0 out of 3 proteins passed
Column 9 between 0 and 0.3 -> 3 out of 3 proteins passed
Column 10 between 0 and 0.2 -> 3 out of 3 proteins passed
0 out of 3 proteins passed in total.

Filtering fold changes in treatment group: Vehicle_1
Column 7 between 0.4 and 0.6 -> 0 out of 3 proteins passed
Column 9 between 0 and 0.3 -> 3 out of 3 proteins passed
Column 10 between 0 and 0.2 -> 3 out of 3 proteins passed
0 out of 3 proteins passed in total.

Filtering fold changes in treatment group: Vehicle_2
Column 7 between 0.4 and 0.6 -> 0 out of 3 proteins passed
Column 9 between 0 and 0.3 -> 3 out of 3 proteins passed
Column 10 between 0 and 0.2 -> 3 out of 3 proteins passed
0 out of 3 proteins passed in total.

Experiment with most remaining proteins after filtering: Treatment_1
-> NormP contains 0 proteins.

Computing normalization coefficients:

1. Computing fold change medians for proteins in normP.
2. Fitting melting curves to medians.
   Error in modelList[[refidx]] :
   attempt to select less than one element in get1index

[MSChemicalGeek]

Hello,

Thanks for using FragPipeTPPR. In order to look at the issue in depth could you provide your tmt-report folder, please? Also, to confirm how many proteins in total does your sample have?

[Sjan1]

Hi, To test the functionality I used data downloaded from your github: FragPipeTPP/inst/extdata/dummyFragPipefolder/tmt-report/ratio_protein_None.tsv at main · Nesvilab/FragPipeTPP<https://github.com/Nesvilab/FragPipeTPP/blob/main/inst/extdata/dummyFragPipefolder/tmt-report/ratio_protein_None.tsv> Clearly, there is not a lot of proteins, but I hoped there are some that shows the melting point difference to test TPP package as well. However, this was just a test. What I care about more are our own data, where I have several problems. First, when I process it with FragPipe I am getting about 10k proteins (20 HPLC fractions pools) but in tmt-report, only contaminant proteins are shown. I believe it is due to parsing of the database, but I cannot find what is wrong. It is Araport11 from Arabidopsis thaliana. Would you look at my fasta file? Another issue is that the experiment was a test - only five temperature points for a ‘control’ and a ‘treatment’ each and no replicates. It is going to be enough to see anything meaningful in TPP? We are talking about proper experiment now but it would encourage us to see we detected some changes. Thanks, Jan --- Jan Sklenar Proteomics support group The Sainsbury Laboratory, Colney Lane, Norwich, NR4 7UH, United Kingdom From: CRojaRam ***@***.***> Sent: 09 December 2024 16:23 To: Nesvilab/FragPipeTPP ***@***.***> Cc: Jan Sklenar (TSL) ***@***.***>; Author ***@***.***> Subject: Re: [Nesvilab/FragPipeTPP] Zero proteins selected (Issue #5) Hello, Thanks for using FragPipeTPPR. In order to look at the issue in depth could you provide your tmt-report folder, please? Also, to confirm how many proteins in total does your sample have? — Reply to this email directly, view it on GitHub<#5 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AC35ILVWPLR6JPVJJ32ZIOD2EW7X5AVCNFSM6AAAAABTIQXGHGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMRYGU2TKMRQGQ>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[MSChemicalGeek]

Hello Jan,

Oh, I seemed to have forgotten to remove those files. They were more to test if the workflow is running fine, and from the output the scripts are running. I will add in the vignette that I recommend using the full dataset. Ok, about your database file, sure. You can send it to me at [email protected]