What is a pep score?
The PEP score is the probability that a peptide (PSM-peptide spectral match) is incorrect. The Sequest score is a calculation that scores and sums each peptide for a given protein. Basically, the higher the score the more confidence you can have that the given peptide identification is correct.
What does PSM mean in mass spec?
of peptide spectrum matches
The number of peptide spectrum matches. The number of PSM’s is the total number of identified peptide spectra matched for the protein.
What is PSM peptide?
A peptide-spectrum match (PSM) scoring function assigns a numerical value to a peptide-spectrum pair (P,S) expressing the likelihood that the fragmentation of a peptide with sequence P is recorded in the experimental mass spectrum S.
What is Q value in mass spectrometry?
Q-value is defined as minimum false discovery rate (FDR). If you search MS/MS spectrum against a decoy database, you know that all PSMs are incorrect. If you search against true databases, you get the mixture of correct and wrong hits.
What are master proteins?
The proteins within a group are ranked according to the number of peptide sequences, the number of PSMs, their protein scores, and the sequence coverage. The top-ranking protein of a group becomes the master protein of that group.
What is protein sequence coverage?
Sequence coverage is simple math, the number of amino acids in a specific protein sequence that were found in the peptides sequenced in your MS/MS study. Duncan Cromarty above went into the confidence that you might have of those peptide to protein assignments.
What is mascot analysis?
Mascot is a software search engine that uses mass spectrometry data to identify proteins from peptide sequence databases. Mascot is widely used by research facilities around the world. Mascot uses a probabilistic scoring algorithm for protein identification that was adapted from the MOWSE algorithm.
What is peptide tolerance?
Peptide mass tolerance indicates the fit of theoretical peptide mass with the experimental measurements, and choice of this parameter sufficiently influences the protein identification. The role of peptide mass tolerance was estimated by counting the number of identified proteins for the reference set of mass-spectra.
What is p-value of protein?
The p-value is a measure of how likely you are to get this protein data if no real difference existed. Therefore, a small p-value indicates that there is a small chance of getting this data if no real difference existed and therefore you decide that the difference in group abundance data is significant.
What is FDR in proteomics?
To control the false positives amongst a set of accepted matches, there is a need for some statistical estimate that can reflect the amount of false positives present in the data processed. False discovery rate (FDR) is the metric for global confidence assessment of a large-scale proteomics dataset.