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Articles tagged: Mascot Distiller

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Posted by John Cottrell (June 17, 2020)

Using the Quantitation Summary to create reports and charts

An earlier article described how to create a Quantitation Summary in Mascot Daemon. This is a spreadsheet-like text file, where the rows correspond to proteins and the columns contain expression data for various samples in the form of abundances or ratios of abundances. A Quantitation Summary can be opened and manipulated in a spreadsheet program such as Excel, and it [...]

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Posted by John Cottrell (May 19, 2020)

Tabulate expression data from multiple analyses with Mascot Daemon

Studies that use mass spectrometry-based quantitation often contain large numbers of individual analyses: samples from different sources or treatments or time points, possibly fractionated, with replicates and so forth. Using statistical methods to combine the analyses, extract meaningful information, and report it as charts and tables is a complex task that usually requires custom scripting in a language such as [...]

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Posted by Ville Koskinen (March 20, 2020)

How to set up remote working

There are times when you unexpectedly find yourself having to work from home. Fear not: data analysis doesn’t need to stop when you’re away from the lab. Mascot Server has a client-server architecture, and the client PC can be located anywhere. Distiller and Daemon can also be used remotely, or they can be run on a remote client PC and [...]

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Posted by John Cottrell (February 19, 2020)

Disulfide bond characterisation

Support for matching crosslinked peptides is a new feature in Mascot Server 2.7. The following linkage types can be detected: intralinks – the linked peptides are from the same protein interlinks – the linked peptides are from two different proteins looplinks – connecting two amino acids within a single peptide monolinks – a linker with one end attached and the [...]

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Posted by Richard Jacob (November 18, 2019)

Disaster recovery

There are a number of potential issues that can cause your Mascot Server or other computer infrastructure to stop working. In the worst case, you may need to do a full recovery from backups. This can be an involved procedure, but it is straightforward as long as you have backed up key configuration and data files. For disk or storage [...]

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Posted by Patrick Emery (August 22, 2019)

The three Ds: Diethylation, Dimethylation and the Deuterium effect

Dimethylation Mascot Server and Mascot Distiller support a number of precursor intensity based quantitation techniques using a number of different techniques and chemistries. The software also allows you to flexibly define your own methods, allowing you to implement quantitation protocols which we have not supplied ‘out of the box’. One isotope labelling method which Distiller supports ‘out of the box’ [...]

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Posted by Patrick Emery (June 20, 2018)

Mascot Distiller 2.7: Farewell to re-gridding

We recently released Mascot Distiller 2.7. The main new feature of this release is a change to how peak detection works on raw profile datasets that have been saved as sparse, or compressed data, with runs of zero values dropped. Common examples of this are Thermo Orbitrap and Sciex Analyst datasets saved as profile data. For these types of data, [...]

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Posted by Ville Koskinen (May 24, 2018)

Higher accuracy for oxidation profiles

Earlier this year, Reest et al. described a quantitation workflow based on light and heavy iodoacetamide labels, which they named SICyLIA [1]. The workflow was used for analysing cysteine oxidation levels between wild-type and redox-stressed mouse cells. At its core, SICyLIA is a precursor protocol with two components, light and heavy, where the labels are simply light and heavy carbamidomethyl on [...]

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Posted by Patrick Emery (February 12, 2018)

MS3 reporter ion quantitation with Mascot Distiller

A common issue encountered when carrying out reporter ion quantitation methods, such as TMT and iTRAQ, is that of interfering ion signals in the reporter region. One commonly used strategy which can be taken to mitigate against this is to reisolate the most abundant ion in the MS/MS spectrum and refragment it. The resultant reporter ion signals in the MS3 [...]

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Posted by Patrick Emery (January 16, 2017)

How many of you are there in there? Processing and searching chimeric MS/MS spectra with Mascot Distiller and Mascot Server

In the typical shotgun proteomics experiment, the assumption is that each MS/MS spectrum is derived from a single precursor selected by the Mass Spectrometer for fragmentation. However, in practice, near isobaric precursors can co-elute and undergo co-fragmentation resulting in chimeric MS/MS spectra containing fragments from multiple different precursor peptides. With high resolution data, it is possible for these overlapping isotope [...]

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