🐛 fix "-" as psm-fdr setting

[enryH]

• allow to have a string value for ProlineStudio as fdr (MBR has no FDR?)
• add minimum and maximum of positives charges specified

@mlocardpaulet It would be great to have at some point a schema specifying allowed values per Software. But I guess the more we test, we will find out which ones are allowed...

[mlocardpaulet]

Huummm... It is true that I don't see anywhere the value for FDR threshold. Anne-Marie indicated that the expected values are:

software tool name and version : Proline 2.2
search engine name and version : Mascot 2.8.3
peaklist generation software tool name and version : MGFBoost 3.6.3 (with eclean)
FDR threshold for PSM, peptide and protein level : 1% PSM
match between run (or not) : yes or no (depends on the file)
precursor mass tolerance : 10ppm
enzyme (although for these data it should be Trypsin) : Trypsin/P
number of missed-cleavages : 2
minimum and maximum peptide length : 7
fixed and variable modifications : cysteine CAM as fixed, methionin oxidation and Protein Nter acetylation as variable
maximum number of modifications : 7
minimum and maximum precursor charge : 2-5

But I don't know where to find these values. I'll ask her Monday.

[enryH]

Huummm... It is true that I don't see anywhere the value for FDR threshold. Anne-Marie indicated that the expected values are:

software tool name and version : Proline 2.2
search engine name and version : Mascot 2.8.3
peaklist generation software tool name and version : MGFBoost 3.6.3 (with eclean) # we don't support that yet
FDR threshold for PSM, peptide and protein level : 1% PSM 
match between run (or not) : yes or no (depends on the file)
precursor mass tolerance : 10ppm
enzyme (although for these data it should be Trypsin) : Trypsin/P
number of missed-cleavages : 2
minimum and maximum peptide length : 7
fixed and variable modifications : cysteine CAM as fixed, methionin oxidation and Protein Nter acetylation as variable
maximum number of modifications : 7
minimum and maximum precursor charge : 2-5

But I don't know where to find these values. I'll ask her Monday.

We don't support: peaklist generation software tool name and version anywhere

We definitely still have some blanks: https://github.com/Proteobench/ProteoBench/blob/fb4d835c43dcdc26d4870c24c9fb34005d5551ba/test/params/ProlineStudio_withMBR.csv

[mlocardpaulet]

Huummm... It is true that I don't see anywhere the value for FDR threshold. Anne-Marie indicated that the expected values are:

software tool name and version : Proline 2.2
search engine name and version : Mascot 2.8.3
peaklist generation software tool name and version : MGFBoost 3.6.3 (with eclean) # we don't support that yet
FDR threshold for PSM, peptide and protein level : 1% PSM 
match between run (or not) : yes or no (depends on the file)
precursor mass tolerance : 10ppm
enzyme (although for these data it should be Trypsin) : Trypsin/P
number of missed-cleavages : 2
minimum and maximum peptide length : 7
fixed and variable modifications : cysteine CAM as fixed, methionin oxidation and Protein Nter acetylation as variable
maximum number of modifications : 7
minimum and maximum precursor charge : 2-5

But I don't know where to find these values. I'll ask her Monday.

We don't support: peaklist generation software tool name and version anywhere

We definitely still have some blanks: https://github.com/Proteobench/ProteoBench/blob/fb4d835c43dcdc26d4870c24c9fb34005d5551ba/test/params/ProlineStudio_withMBR.csv

Thanks. I'll discuss these "blanks" with Anne-Marie. I think that there are too many and it comes from missing information in their outputs.