Fengchao

This is a bug reported by emails. I put it here in case we forget it. It also let potential affected users know: human contaminant proteins are always not marked...

Spectral library generation part is using more threads that it is supposed to be

6

The EasyPQP `convert` command seems to be multithreading: each command is using all CPU cores. But the `gen_con_spec_lib.py` script also execute multiple `convert` commands in parallel, which makes the total...

Let Philosopher print errors when there are protein hits from PSMs that cannot be found in the fasta file.

1

This is a bug/feature I found by accident (https://github.com/Nesvilab/FragPipe/issues/537#issuecomment-995943414). Basically, when you search the data with FASTA file A, and run Philosopher to filter the result using FASTA file B,...

The razor assignment might make an alternative protein as the razor protein. Since we don't distinguish `I` and `L` in the protein mapping, some peptides might not exist in their...

Normalized retention time need to be restricted in the range

3

Hi Guo Ci @guoci , There are outliers in normalized retention time (out of [-100, 200]). It looks like the range needs to be restricted in the range during the...

There are zero intensity peaks in the spectral library built by easypqp

5

Hi Guo Ci @guoci , This is an issue from users. They find that some fragments in the spectral library have zero intensity. Could you please follow up and fix...

I added some codes to support "()" style modification. I tested it with one pin file and changed all the "[]" to "()" style. Percolator produced the same result. Please...

请@hidetag来这里讨论别你关掉的你自己的那个issue

27

issue贴在这里，我还没回复完那人就关了。说好的道德高点呢？说好的开源精神呢？ https://github.com/houshanren/hangzhou_house_knowledge/issues/131

北上广深各来一波？

3

妥妥地包揽Trending前五

Let Philosopher print errors when there are protein hits from PSMs that cannot be found in the fasta file.

1

This is a bug/feature I found by accident (https://github.com/Nesvilab/FragPipe/issues/537#issuecomment-995943414). Basically, when you search the data with FASTA file A, and run Philosopher to filter the result using FASTA file B,...