FragPipe

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Fragpipe runs PTMShepherd without it being enabled and then results in exit code 1?

1

[log_2024-07-03_05-17-39.txt](https://github.com/user-attachments/files/16084990/log_2024-07-03_05-17-39.txt) **- Describe the issue or question:** After running through most of a search, fragpipe opened PTMShepherd and ran a series of commands culminating in exit code "1". The thing...

vikascinderbio

Difficulty in analyzing DIA data using DIA-NN

1

**- Upload your log file** I am trying to analyze DIA data but the analysis crashes before running DIA-NN for quantification due to an issue with the spectral library. **-...

RonenGabizon

Error "java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space

1

Good morning, As I show in the attached log file, I get the error "java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space". [log_2024-07-01_17-12-54.txt](https://github.com/user-attachments/files/16065194/log_2024-07-01_17-12-54.txt) I have tried setting Workflow > Global settings, RAM =...

VirginiaCarayol

LFQ-phospho - sequence

2

Will you be able to extract the sequence window more flexibly? Could you get the predicted phosphosite in the middle of the window, so we can get the sequence of...

ghost

Summary table-like output for FragPipe

1

Hi all, For QC purposes it would be nice to have a similar summary table as MaxQuant [currently](https://cox-labs.github.io/coxdocs/output_tables.html#summary-table) outputs but from what I can tell nothing similar is output. Certainly...

carlosg-czbiohub

FP 22.0, plexDIA & MSBooster

4

[log_2024-06-19_10-51-42.zip](https://github.com/user-attachments/files/15898278/log_2024-06-19_10-51-42.zip) Hi, I am using FragPipe 22.0 on a triplex plexDIA (L=+28, M=+32, H=+36 Da, semi-specific Nt. search strategy with ArgC) HUNTER sample, measured on an Exploris480 with FAIMS and...

kabalak

SaintExpress Analysis after GPF-DIA?

1

 I am trying to run SAINT analysis after searching CONTROL (n=4) vs GENE1 (n=4) in my AP-MS dataset. I am using GPF-DIA data and have loaded the DIA-Umpire_Spec_Quant Workflow...

TTCooper-PhD

FragPipe v22 + DIA-NN 1.9 - Failed to generate skyline document

3

Hi Fengchao, I'm trying to set up a DIA_SpecLib_Quant proteomic workflow using the latest versions of FragPipe and DIA-NN. The run finishes with DIA-NN output files however, I keep getting...

emhumphries

Peaks with unreasonable large mz broke MSFragger

4

**- Upload your log file** (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation,...

amingson

Failed in reading frame (intensity is larger than the maximum allowed value)

2

Hi, I was running FragPipe workflow for timsTOF data. However it finished with the following error message: ``` 2024-06-02 19:58:08 [INFO] - Loading \\msdirect13\share\share\timsTOF\2024-05\240502RT\240502RT_trypsin_1_1_1_682.d... 2024-06-02 19:58:13 [INFO] - ...20%...40%...60%...2024-06-02 19:59:38...

tomi3636