I finnaly find how to interrogate dabases/ spectra with unspecific leavage on SearchGUI. Nevertheless, the output files were not read by Proline. When I tried to import it, I have this error message : code 32002"reqirement failed : unexpected number of enzyme"

Is there an additional action to do on proline to authorize the search?

Thanks a lot,

Regards,

Chloé

I regularly use proline for proteomic analysis.

I would like to use it for peptidomic analysis, and, in SearchGui, it is not possible to choose "No enzyme". Do you have an idea of the parameters to use if we want to search extreted peptides in sample without any digestion step?

More and more peptidomic studies coming out and it is unclear about how they perform the search. I would like to know if you have already think about that and what would be the possibilities offer by proline to process this kind of samples?

Thank alot for your answer,

Regards,

Chloé

Concerning the parsing_rules file, it is configured using regular expression (java one). To create a valid regular expression the RegEx site is very helpful.
We will give you here 3 examples of parsing rules

1. Case one : Uniprot file. Suppose your fasta file are formatted like : uniprot_<someTextWithOUT'_'>_2017_02.fasta. In these files, entries are
   >sp|P53319|6PGD2_YEAST 6-phosphogluconate dehydrogenase, decarboxylating 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=GND2 PE=1 SV=1 and protein name to extract is 6PGD2_YEAST
2. Case two: Uniprot file 2. Suppose your fasta file are formatted like : UP_<someTextWithOUT'_'>_20170225.fasta. In these files, entries are
   >sp|P53319|6PGD2_YEAST 6-phosphogluconate dehydrogenase, decarboxylating 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=GND2 PE=1 SV=1 and protein name to extract is P53319
3. Case three: TAIR file. Suppose your fasta file are formatted like : TAIR10_<anyText>.fasta. In these files, entries are
   >AT1G51380.1 | Symbols:  | DEA(D/H)-box RNA helicase family protein | chr1:19047960-19049967 FORWARD LENGTH=392 and protein name to extract is AT1G51380.1

the parsing rules should be :

parsing-rules = [{
   name="uniprot1",
  fasta-name=,                                       // all files which name start with 'uniprot' will be considered by this rule
  fasta-version="uniprot _(*)_(.*).fasta",   // uniprot version will be extract from second '_' to the end of the file name. 2017_02 in Case 1
  protein-accession =">\\w{2}\\|*\\|(\\S+)" //extract last part of the entry as accession. 6PGD2_YEAST in Case 1
},
{
  name="uniprot2",
  fasta-name=,                                           // all files which name start with 'UP_' will be considered by this rule 
  fasta-version="UP_*_(.*).fasta",             // uniprot version will be extract from second '_' to the end of the file name. 20170225 in Case 2
  protein-accession =">\\w{2}\\|(+)\\|" //extract second part of the entry as accession. P53319 in Case 2
},
{
  name="TAIR",
  fasta-name=,                                  // all files which name start with 'TAIR' will be considered by this rule 
  fasta-version="TAIR(*)_.*.fasta",    // TAIR version is extract after TAIR word and before first '_'
  protein-accession =">(\\S+)"                    // Protein accession is extract from beginning to first space
}]

Open a command line window in the directory containing raw2mzdb.exe (where archive file have been unzipped) 
Type:
raw2mzdb.exe -i <rawfilename> -o <outputfilename>

By default, the raw file will be converted in the “fitted” mode for the MS1 (MS2 is often in centroid mode and cannot be converted in fitted mode). If the MS2 (or superior) are acquired in high resolution (i.e in profile mode), you could specify that you want to convert several MSs in the required mode: 
raw2mzdb.exe -i <rawfilename> -o <outputfilename> -f 1-2 will try to convert MS1 to MS2 in fitted mode. 

There are two other available conversion modes: 

1. “profile”, the command line is then: raw2mzdb.exe -i <rawfilename> -o <outputfilename> -p 1 (means you want profile mode for MS1, others MS will be stored as they were stored in the raw file)
2. “centroid” : raw2mzdb.exe -i <rawfilename> -o <outputfilename> -c 1 (means you want centroid mode for MS1, others MS will be stored as they were stored in the raw file)

Ensure your regional settings parameters are '.' for the decimal symbol and ',' for the list separator