SELPHI | Systematic Extrapolation of Linked Phospho-Interactions

SELPH-Convert (Beta)

Welcome to SELPH-Convert! Please be advised that this service is in beta, so always check your results and please let us know if you find errors.

Before use please read the instructions for each field by hovering over the These signs will give you more information about each parameter. sign, or by expanding the instructions tab.

Important: SELPH-Convert does not accept Excel files (.xls or .xlsx) at this stage. Before you submit your file, if it is not in text tab- or comma-delimited, format please go to: File-> Save As-> and select either "Comma Separated values .csv" or "Tab-delimited text .txt". The first line of your file MUST contain the headers for your columns.

Job Information

Please upload your file first.

Job Information

Jobname*

Sample Tag

Data File Generation

Select the title of the column that contains the name of your identified proteins. e.g. if your files were generated by MaxQuant, this would be the 'Leading Protein' column. Make sure the column label is provided as is in the file.

Protein Label*

Select the title of the column that contains the identified phosphopeptides. e.g. if files were generated by MaxQuant, this would be the 'Modified Sequence' column. If you used Mascot this would probably be the 'Peptide sequence' column.

Peptide Label*

If your peptides above don't contain the modified residues e.g. _RGFSPpTGQ_ or RGFSPT(ph)GQ you need to provide the location of the site in the peptide. e.g. for Mascot output select: 'Variable Modifications'.

Phosphosite Location
Detailed Explanation

No amino acid Column contains only the phosphosite index as number (e.g. 235)

With amino acid Column contains the residue and the phosphosite index as number (e.g. S235)

Some outputs or published data files may not contain the peptide phosphorylation sites in the peptide sequence but may provide them in a separate column. You only need to select an option in this tab if your peptides provided above did NOT contain the phosphorylation site. In this case you must select from your headers the column that contains this information and choose one of the two options: If the column contains the sites with the amino acid, e.g. Y45 you must select the option that says 'with amino acid'. If it only contains the number e.g. 45 then select the option that says 'no amino acid'.

Data*

Intensity

If you want your identical peptide identifications to be weighted by Peptide Score please provide the label of the column containing this score.

Score label

Phospho-map File Generation

Detailed Explanation

For faster SELPHI runs or if you don't have the database file in FastA format that was used to perform the search that mapped your spectra to peptides/proteins you will need to provide SELPHI with a phosphorylation map file.

Some report or published files provide either (1) the start location of each peptide in the protein sequence, or (2) the position of the first phosphorylation site of each identified phospho-peptide in the sequence. In the first case you need to select the appropriate column in the 'Peptide Start' tab below. Note that this will only work if you have provided peptides with phosphosites annotated (e.g. _RGFSPpTGQ_ or RGFSPT(ph)GQ) or if you have selected a column in the 'Phosphosite Location' above. In the second case you can ignore the 'Peptide Start' tab and choose a column in the 'Phosphosite Global Position' tab. You do NOT need to provide both. If you select a column in the 'Phosphosite Location' tab you must choose one of the two options: If the column contains the sites with the amino acid, e.g. Y45 you must select the option that says 'with amino acid'. If it only contains the number e.g. 45 then select the option that says 'no amino acid'.

Please select the column that indicates the start location of your peptide in the protein sequence. Only if the peptides you provided contain the phosphosite (e.g. _RGFSPpTGQ_ or RGFSPT(ph)GQ) or you have selected a column in the 'Phosphosite Location' tab above.

Peptide Start

Phosphosite Global Position

No amino acid Column contains only the phosphosite index as number (e.g. 235)

With amino acid Column contains the residue and the phosphosite index as number (e.g. S235)

ID Map File Generation

Detailed Explanation

For faster SELPHI runs or if you don't have the database file in FastA format that was used to perform the search that mapped your spectra to peptides/proteins you will need to provide SELPHI with an IDmap file. For this you must select the species that your samples were collected from and it would be very helpful if there are additional columns in your report file that indicate what the ID of your protein will be. Examples of such columns could be 'Gene Names', 'Protein description' etc. You can select more than one column in this field. SELPH-Convert also produces an 'idsnotmapped' file. You can manually, or using Uniprot's or BioMart's ID mapper assign ids to these proteins if you wish and append them to the idmap file so that you can submit as complete an idmap to SELPHI as possible. If you don't fill these missing ids in, these proteins will be ignored for the Pathway and GO term analyses but will be used in the rest of the analyses.

Species

Please select additional columns in your file that could help the id mapping, e.g. Gene Name column, Protein description column etc. Use the CTRL and SHIFT keys to make multiple selections.

Additional Name Info

Name Type

I am providing UniprotKB AC, ID or Gene Name