Blog

Posted by John Cottrell (July 14, 2021)

Error tolerant searches now show statistical significance

The latest release of Mascot Server introduces some important changes to error tolerant searches. Matches from the second pass search now have expect values attached, indicating confidence levels. These are either estimates based on counting trials or empirical values derived from searching a decoy database. If you are not familiar with the error tolerant search, now is the time to [...]

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Posted by Ville Koskinen (June 17, 2021)

NCBI nr tips

NCBI nr is the comprehensive database of non-identical protein sequences compiled by the National Center for Biotechnology Information. The database is available in Mascot Server as the NCBIprot predefined definition. If possible, nr should be used as the database of last resort due to its huge size. The January 2021 version contains 338 million protein sequences and the FASTA file [...]

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Posted by Patrick Emery (May 24, 2021)

Improving precursor quantitation results with ion mobility filtering

One of the major new features in Mascot Distiller 2.8 is support for raw data files from the Bruker timsTOF instrument. timsTOF combines an ion mobility dimension with QTOF, allowing an additional separation dimension. The instrument can use this to help separate MS/MS spectra from otherwise isobaric peptides. Mascot Distiller 2.8 can use the precursor ion mobility values for identified [...]

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Posted by Patrick Emery (April 28, 2021)

Global thinking: Label Free Quantitation in Mascot Distiller 2.8

Mascot Distiller supports a wide range of precursor based quantitation methods, including two label-free methods, which we call Replicate and Average. Version 2.8 makes significant improvements to the Replicate method. This is the method for label-free quantitation based on the relative intensities of extracted ion chromatograms (XICs) for precursors in multiple data sets aligned using mass and elution time. Replicate [...]

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Posted by Ville Koskinen (March 17, 2021)

How much cashmere is in this sweater?

Textiles made from luxurious animal hair like cashmere and angora can fetch a high price. Bloomberg reported that cashmere garments alone were worth $1.4 billion in global exports in 2016. Big money attracts fraudsters, and sometimes products claiming to be cashmere could be something else, like rat fur. In this context, the International Organization for Standardization (ISO) has recently standardised [...]

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Posted by Ville Koskinen (February 24, 2021)

Unipept and Mascot

Drawing conclusions from protein-level data is complicated in environmental and metaproteomics studies, where the sample is a mixture of hundreds or thousands of proteomes. The Unipept database is a useful, complementary resource for interrogating metaproteomics data and can be used in conjunction with Mascot’s protein inference. Human gut example Identify proteins by more than ‘gut’ feeling discussed analysing a human [...]

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Posted by Patrick Emery (January 21, 2021)

NIST Human HCD Spectral Libraries

Mascot 2.6 and later can search spectral libraries using the MSPepSearch spectral library search engine from the US National Institute of Standards and Technology (NIST). Spectral libraries can be searched alongside FASTA sequence databases to give an integrated report, and you can easily generate spectral libraries from your own search results. When we introduced spectral library searches in Mascot 2.6, [...]

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Posted by Richard Jacob (December 22, 2020)

How large a Mascot Server licence do I need?

One frequent question from new customers is how many CPUs do I need to licence for my Mascot Server? This is actually two questions. First, Mascot is licensed in CPU units, where 1 CPU is good for 4 cores. The computer can have more than one processor, and each processor can have more than 4 cores, but only the number [...]

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Posted by Ville Koskinen (November 18, 2020)

Single sign-on (SSO) and Mascot

Mascot Server has a role-based security system called Mascot Security. Common use cases are restricting access to configuration files or specific sequence databases, or imposing limits on search size or duration for specific users or groups. These were discussed in earlier blog articles Mascot Security: priority settings and Mascot Security: privacy settings. Mascot Security isn’t designed to have super secure [...]

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Posted by John Cottrell (October 19, 2020)

Solving a puzzle with Mascot Distiller de novo

Have you tried either of the MS/MS interpretation challenges organised by EUPA and LBMSDG? Maybe you are expert enough to read off the peptide sequence, directly. If so, you can stop reading right here! If your interpretation skills and mental arithmetic are a bit rusty, we thought it might be useful to walk through how Mascot Distiller plus a bit [...]

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Posted by Richard Jacob (September 16, 2020)

The minutiae of database management

The two major inputs into a database search are sequence databases and mass spectrometry data. Management of the databases in Mascot Server has evolved and improved over the years and newer versions. There are still a few issues that come up regularly and I am going to cover them in this article. Common error messages When you activate a new [...]

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Posted by Ville Koskinen (August 19, 2020)

Validating intact crosslinked peptide matches

Intact crosslinked search results are more complex than conventional (non-crosslinked) searches, because there are many more degrees of freedom. The precursor mass could be within tolerance of a looplinked sequence, a linear sequence with monolink and several different alpha-beta candidates. Each possibility is multiplied if you also consider variable modifications like oxidation of methionine. Mascot 2.7 uses the same scoring [...]

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