Blog

Posted by John Cottrell (November 15, 2018)

The plus one dilemma

There are several common modifications that can add approximately 1 Da to a peptide mass. Even if you have high accuracy data, it can sometimes be difficult to figure out which one is correct.   Delta Lys->Glu substitution 0.947630 Leu->Asn or Ile->Asn substitution 0.958863 Deamidation at N or Asn->Asp substitution 0.984016 Deamidation at Q or Gln->Glu substitution 0.984016 Citrullination at [...]

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Posted by Patrick Emery (October 15, 2018)

Back to basics 3: Quantitation statistics

Mascot Server and Distiller support a number of different quantitation methods. These methods are carried out at the peptide level, the peptides are then grouped into protein families, and the peptide quantitation results used to calculate protein ratio values. Mascot and Distiller perform a number of statistical procedures and tests to give you an indication of the quality and reliability [...]

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Posted by John Cottrell (September 18, 2018)

Mascot Server cluster mode

Most modern Intel processors have at least 4 cores and some models have 12 cores or more. Mascot Server is licenced by the CPU, where each CPU corresponds to 4 physical cores, so a single PC is perfectly sufficient for licences of 1 or 2 CPU. If you have a larger licence, there comes a point where it is not [...]

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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 Richard Jacob (July 16, 2018)

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 [...]

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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 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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