1. Each results report will contain:
Chromatogram for sample
All proteins identified with probability <1.0
List of peptides identified for each protein
Amino acid coverage of each protein identified
Reported as Excel file
Example of a chromatogram (peptide with 12.6 min retention time highlighted in red)

2. Example of proteins identified in sample
P (Probability) Sf
Score MW
Accession #
Peptide (Hits) 1
Tetranectin precursor
2.07 x 10-11
30.56
206.40
IPI
270 ( ) 2
Isoform 1 of Protein kinase C theta type
1.16 x 10-3
2.23
52.18
IPI
68 ( )
Probability – lower the number, the higher the probaility of a match
Sf – final score indicates how good the protein match is
Score – Value based on the probability that the peptide is a random match to the spectral data
MW – Molecular weight of the protein
Accession # - Unique protein identification number for the sequence
Peptide (Hits) – Total number of peptide matches
Example of amino acid sequence coverage (in red) of a protein identified in sample

3. Example of Excel file included in a report
Example of Excel file included in a report. Protein parameters are shaded in grey. Includes peptides (partial list shown) identified for that protein
Protein Identification
(P) Probability – lower the number, the higher the probaility of a match
Sf – final score indicates how good the protein match is
Score – Value based on the probability that the peptide is a random match to the spectral data
MW – Molecular weight of the protein
Accession # - Unique protein identification number for the sequence
Peptide (Hits) – Total number of peptide matches
Peptide Identification
MH+
P(pep) Sf XC
DeltaCn Sp
RSp
Ions
Count

4. Protein and peptide parameters of the results
(grey shade)
P, Probability for protein (pro) or peptide (pep) – lower the number, the higher the probability of a match
Sf – final score indicates how good the protein or peptide match is
Score – Value based on the probability that the peptide is a random match to the spectral data
MW – Molecular weight of the protein
Accession # - Unique protein identification number for the sequence
Peptide (Hits) – Total number of peptide matches
Peptide
MH+ - molecular weight of the peptide
XC - Cross-correlation value between observed and theoretical peptide fragment mass spectrum
DeltaCn – change in cross-correlation between the first and the nth peptide match, where n = peptide hit number
Sp – Preliminary score, % of peptide fragment ions in MS/MS spectrum that match with the experimental data
Rsp – Ranking of match during Sp scoring
Ions – Matched ions/Total number of theoretical ions
Count – Number of duplicate entries per .dta file

5. MS/MS fragment ion matches for peptide fragment K. NWETEITAQPDGGK
MS/MS fragment ion matches for peptide fragment K.NWETEITAQPDGGK.T with 12.6 min retention time. Specific fragment ion matches can be included in report at your request.
The list of B and Y ions as they match against the experimental data
(matched B ions – red, matched Y ions – blue)
The mass errors of the measurement.
MS/MS data of fragment ions that matched theoretical data of database