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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 (April 14, 2020)

Human Proteome Project data interpretation guidelines

The Human Proteome Project (HPP) data interpretation guidelines were recently updated. Many of the guidelines are good practice and common sense in any proteomics study where reliable protein identification is critical, not just when studying the human proteome. The guidelines are easy to meet using Mascot Server 2.7. Core guidelines The full list consists of 9 guidelines. The first one [...]

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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 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 (February 15, 2017)

Exporting search results: tips and tricks

The Mascot Server export utility allows search results to be exported in a wide range of formats, together with the native result file and the MGF peak list. Exporting the result file can be useful if you need it for a third party application and don’t have file share access to the Mascot Server. Exporting the MGF might be useful [...]

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Posted by Ville Koskinen (October 21, 2015)

PSI file formats, part 4: mzTab

mzTab is a relatively new file format for reporting protein and peptide search results. Its specification (1.0) was published in June 2014. Like mzIdentML, it is developed by the Proteomics Standards Initiative (PSI) and shares some of the same controlled vocabulary (CV). However, that’s where the similarities end. The biggest differences are that mzTab is table-based text, not XML, and [...]

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Posted by Ville Koskinen (August 15, 2015)

PSI file formats, part 3: repositories

We’ve talked about mzIdentML validity only in terms of file structure. Proteomics repositories, such as PRIDE or ProteoRed, of course require files to be valid in that sense, but they impose additional requirements. If you need to upload your search results to a repository, it is worth looking at this more extended idea of validity. For simplicity, I’ll only consider [...]

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Posted by Ville Koskinen (June 17, 2015)

PSI file formats, part 2: validation

The first part listed a number of ways for generating mzIdentML files and named a few pieces of software capable of reading and processing them. This part of the series discusses a rather technical issue with mzIdentML files, namely validity, and how it can affect you as a user. Validation is somewhat tangled with submitting mzIdentML files to proteomics repositories, [...]

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Posted by Ville Koskinen (May 14, 2015)

PSI file formats, part 1: mzIdentML

Mascot search results are saved in a .dat format, which contains all protein and peptide identifications output by Mascot, as well as auxiliary information (search parameters, mass definitions for modifications, etc.). The .dat file is almost never the final step in data analysis; for the next step, you need to import the search results in some other piece of software. [...]

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