Using ProPhosSI
ProPhosSI takes a putative peptide match and the associated MS/MS spectrum and provides an analysis of the match. In order to do this it requires information about the peptide and the MS/MS spectrum. Explanatory information for each field in the form is given below.Report details:
- Search title
- Enter a title for this particular peptide spectrum match
- Ion match tolerance
- The maximum delta mass to call an observed and theoretical ion pair a match.
- Ion intensity threshold
- Minimum relative intensity of an ion to be considered signal rather than noise. Ions below this level are ignored in the analysis (though matches are reported).
- Ion series to annotate
- Select the ion series you wish to be shown on the spectrum plot
- Spectrum image width
- Size of the spectrum image embedded int he HTML report
Peptide details:
- Protein name
- Name/identifier for the protein containing the matched peptide
- Match score
- Score given by the search engine identifying this peptide hit (not essential)
- Missed cleavages
- Number of missed digestion sites in the peptide (not essential)
- Peptide sequence
- Amino acid sequence in single letter code. This may be surrounded by the previous and following amino acids in X.YYYYYYY.Z format
- Protein start/end
- Start and end amino acid positions for the peptide in the protein
- Cysteine modification
- Cysteine residues are typically alkylated prior to digestion and subsequent analysis. Select the appropriate method to ensure that the correct mass is used for the cysteine derivative.
- SILAC delta mass
- For peptides grown in isotopically labelled media, enter the delta mass for the lysine and/or arginine residues
- Post-translational modifications
- Enter post-translational modifications, one per line in the following form:
position modification
For example, for a phosphopeptide with a phosphate on position 16, enter
16 Phospho (STY)
The modification must be one of the types known to ProPhosSI (UniMod names, not hidden plus several related to Ubiquitination)- Acetyl (K)
- Acetyl (N-term)
- Acetyl (Protein N-term)
- Biotin (K)
- Biotin (N-term)
- Carbamidomethyl (C)
- Carbamyl (K)
- Carbamyl (N-term)
- Carboxymethyl (C)
- Cation:Na (DE)
- Deamidated (NQ)
- Dehydro (C)
- Dioxidation (M)
- Ethanolyl (C)
- ExacTagAmine (K)
- ExacTagThiol (C)
- Formyl (N-term)
- Formyl (Protein N-term)
- Guanidinyl (K)
- ICAT-C:13C(9) (C)
- ICPL (K)
- ICPL (Protein N-term)
- ICPL:13C(6) (K)
- ICPL:13C(6) (Protein N-term)
- ICPL:13C(6)2H(4) (K)
- ICPL:13C(6)2H(4) (Protein N-term)
- ICPL:13C(6)2H(4) (N-term)
- ICPL:2H(4) (K)
- ICPL:2H(4) (Protein N-term)
- iTRAQ4plex (K)
- iTRAQ4plex (N-term)
- iTRAQ4plex (Y)
- iTRAQ8plex (K)
- iTRAQ8plex (N-term)
- iTRAQ8plex (Y)
- Methyl (DE)
- Methyl (DE)
- Methylthio (C)
- mTRAQ (K)
- mTRAQ (N-term)
- mTRAQ (Y)
- mTRAQ:13C(3)15N(1) (K)
- mTRAQ:13C(3)15N(1) (N-term)
- mTRAQ:13C(3)15N(1) (Y)
- NIPCAM (C)
- Oxidation (M)
- Oxidation (HW)
- Oxidation (HW)
- Phospho (ST)
- Phospho (ST)
- Phospho (Y)
- Propionamide (C)
- Pyridylethyl (C)
- Sulfo (S)
- Sulfo (T)
- Sulfo (Y)
- TMT (K)
- TMT (N-term)
- TMT2plex (K)
- TMT2plex (N-term)
- TMT6plex (K)
- TMT6plex (N-term)
- Pyro-glu (N-term E)
- Phospho (STY)
- N-Acetyl (Protein)
- Sulphone (M)
- Pyro-glu (N-term Q)
- Pyro-glu (N-term Q)
- Gln->pyro-Glu (N-term Q)
- HexNAc (N)
- GlyGly (K)
- LeuArgGlyGly (K)
- GlyGly (N-term)
Spectrum details:
- Parent ion m/z
- The observed parent ion m/z in the primary scan
- Charge
- The calculated charge for the observed parent ion m/z
- Ion list:
- The ions should be listed one per line with the m/z followed by the intensity
Example:
643.25 1034.5