Blog

Posted by Ville Koskinen (April 13, 2018)

Keeping genome databases up to date

Database Manager is a great tool for keeping your sequence databases up to date in Mascot. If the database is available as a ready-made FASTA file, all you need to do is enable it as a predefined definition, or set up a definition to download the file from a known URL (see the help for more details). Updating the database [...]

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Posted by John Cottrell (March 14, 2018)

Stepping up security

In late 2016, NCBI dropped support for HTTP requests and restricted their web resources to HTTPS. EBI went HTTPS by default in October 2017 and UniProt has announced that it will go HTTPS-only in June 2018. The UniProt change will cause a problem with Database Manager in older versions of Mascot. This article summarises the effects of turning off HTTP, [...]

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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 John Cottrell (January 12, 2018)

Results round-up for the ‘dark matter’ challenge

In June, we tried to harness the power of crowd-sourcing to explain some of the unidentified modifications found in open database searches. We selected 20 abundant and unassigned mass deltas from Supplementary Table 3 of the recent MSFragger paper from Alexey Nesvizhskii’s group at U. Michigan and offered prizes for the first credible explanations. There were 35 unannotated deltas in [...]

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Posted by John Cottrell (December 12, 2017)

A quarter-century in 2018

That a protein could be identified from the masses of the peptides obtained on its digestion with a specific protease was recognised semi-independently by several research groups. An example of morphic resonance? Or, an idea whose time had come? Most likely, it was just one of many ideas that floated around within the small community studying proteins and peptides by [...]

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Posted by Richard Jacob (November 16, 2017)

Using a shared TaskDB with Mascot Daemon

Mascot Daemon is our automation client for Mascot Server. The client was introduced with Mascot Server version 1.6 and has been continually developed ever since. The licensing for Mascot Daemon allows as many copies of Daemon to be installed in your lab as you like. By default, each copy of Daemon uses its own task database, TaskDB, to store information [...]

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Posted by John Cottrell (October 16, 2017)

Step away from the iodoacetamide

In our July newsletter, we featured a paper from Torsten Müller and Dominic Winter, University of Bonn, concerning alkylation artefacts. Some of their findings were quite shocking. For example, differences of more than 9 fold in numbers of identified methionine-containing peptides for in-gel digested samples between iodine- and non-iodine-containing alkylation reagents. This is important because a glance at the literature [...]

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Posted by John Cottrell (September 12, 2017)

How to create a spectral library for contaminants

An earlier article highlighted how modified and non-specific peptides from contaminants can be matched using a spectral library without increasing the search space for the target proteins. This is particularly useful for sequencing grade trypsin, which is modified by methylation or acetylation of the lysines, creating a large number of modified non-specific peptides that are missed by typical search strategies. [...]

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Posted by Ville Koskinen (August 12, 2017)

Exporting spectral library search results

Mascot 2.6 integrates spectral library searching. Today we’ll describe how these searches can be exported. Please ensure you’ve installed the Mascot 2.6.1 patch, as support for exporting library search data was not complete in the initial Mascot 2.6.0 release. Library searches can be either library-only or integrated searches. Integrated means the search is against both a spectral library and a [...]

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Posted by John Cottrell (July 12, 2017)

The most analysed protein is …

Trypsin, of course. The Journal of Proteome Research has a paper from the Medical University of Graz concerning the importance of correctly identifying spectra from contaminant proteins. In particular, trypsin autolysis peptides. The authors point out that sequencing grade trypsin is modified by methylation or acetylation of the lysines, to inhibit autolysis. Unless these variable modifications are selected in a [...]

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Posted by John Cottrell (June 26, 2017)

Trying to illuminate proteomics ‘dark matter’

The May 2017 issue of Nature Methods has a paper from Alexey Nesvizhskii’s group at U. Michigan describing a new open database search program called MSFragger. Strikingly, they also observed the two highly abundant but unidentified mass deltas reported in Steven Gygi’s 2015 mass tolerant paper: 301.9864 and 249.9803. The challenges of open searching were discussed in an earlier blog [...]

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