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Posted by Ville Koskinen (September 16, 2019)

Common myths about protein scores

Mascot Server is used in many different application areas by both mass spectrometry experts and non-experts. Over the years, we’ve spotted a few recurring misconceptions about how protein scores are interpreted and used. All the examples come from recent peer-reviewed papers. Protein scores in PMF searches The very first thing to check is, what type of experiment is being reported. [...]

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Posted by David Creasy (August 17, 2018)

Back to Basics 2: Common mistakes

When a search on our public web fails, we are often contacted to provide some help. These are some of the common mistakes we have seen. Most of the focus here is on Peptide Mass Fingerprint (PMF) searches, which are still very popular on our public web site. If you are new to database searching, you may find this tutorial [...]

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Posted by John Cottrell (March 6, 2013)

When to use Combination searches

Most database searches are either Peptide Mass Fingerprints, with a list of peptide molecular mass values, or MS/MS searches, where the mass of each peptide precursor is only used to filter candidate sequences from the database before scoring matches for the fragments. It is also possible to combine the two, in a so-called Combination search, where both the molecular mass [...]

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