Blog
Back to Basics: Optimize your search parameters
Every now and then you need to determine good search parameters for a data set. They may be different from the normal ones you use due to a change in instrumentation, you may be analyzing data from a public resource like PRIDE/Proteome exchange or it could be data from a collaborator. Whatever the reason, here’s a quick overview on how [...]
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, [...]
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 [...]
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 [...]
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, [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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. [...]
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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