Blog
Global thinking: Label Free Quantitation in Mascot Distiller 2.8
Mascot Distiller supports a wide range of precursor based quantitation methods, including two label-free methods, which we call Replicate and Average. Version 2.8 makes significant improvements to the Replicate method. This is the method for label-free quantitation based on the relative intensities of extracted ion chromatograms (XICs) for precursors in multiple data sets aligned using mass and elution time. Replicate [...]
How much cashmere is in this sweater?
Textiles made from luxurious animal hair like cashmere and angora can fetch a high price. Bloomberg reported that cashmere garments alone were worth $1.4 billion in global exports in 2016. Big money attracts fraudsters, and sometimes products claiming to be cashmere could be something else, like rat fur. In this context, the International Organization for Standardization (ISO) has recently standardised [...]
Unipept and Mascot
Drawing conclusions from protein-level data is complicated in environmental and metaproteomics studies, where the sample is a mixture of hundreds or thousands of proteomes. The Unipept database is a useful, complementary resource for interrogating metaproteomics data and can be used in conjunction with Mascot’s protein inference. Human gut example Identify proteins by more than ‘gut’ feeling discussed analysing a human [...]
NIST Human HCD Spectral Libraries
Mascot 2.6 and later can search spectral libraries using the MSPepSearch spectral library search engine from the US National Institute of Standards and Technology (NIST). Spectral libraries can be searched alongside FASTA sequence databases to give an integrated report, and you can easily generate spectral libraries from your own search results. When we introduced spectral library searches in Mascot 2.6, [...]
How large a Mascot Server licence do I need?
One frequent question from new customers is how many CPUs do I need to licence for my Mascot Server? This is actually two questions. First, Mascot is licensed in CPU units, where 1 CPU is good for 4 cores. The computer can have more than one processor, and each processor can have more than 4 cores, but only the number [...]
Single sign-on (SSO) and Mascot
Mascot Server has a role-based security system called Mascot Security. Common use cases are restricting access to configuration files or specific sequence databases, or imposing limits on search size or duration for specific users or groups. These were discussed in earlier blog articles Mascot Security: priority settings and Mascot Security: privacy settings. Mascot Security isn’t designed to have super secure [...]
Solving a puzzle with Mascot Distiller de novo
Have you tried either of the MS/MS interpretation challenges organised by EUPA and LBMSDG? Maybe you are expert enough to read off the peptide sequence, directly. If so, you can stop reading right here! If your interpretation skills and mental arithmetic are a bit rusty, we thought it might be useful to walk through how Mascot Distiller plus a bit [...]
The minutiae of database management
The two major inputs into a database search are sequence databases and mass spectrometry data. Management of the databases in Mascot Server has evolved and improved over the years and newer versions. There are still a few issues that come up regularly and I am going to cover them in this article. Common error messages When you activate a new [...]
Validating intact crosslinked peptide matches
Intact crosslinked search results are more complex than conventional (non-crosslinked) searches, because there are many more degrees of freedom. The precursor mass could be within tolerance of a looplinked sequence, a linear sequence with monolink and several different alpha-beta candidates. Each possibility is multiplied if you also consider variable modifications like oxidation of methionine. Mascot 2.7 uses the same scoring [...]
Variable Modifications in Mascot 2.7
Most protein samples will exhibit some degree of modification which needs to be considered when carrying out a database search In this article we’ll take a look at some important changes we introduced in Mascot 2.7 in how Mascot handles variable modifications. Variable modification permutation in Mascot 2.6 and earlier In Mascot 2.6 or earlier, variable modification permutation is handled [...]
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 [...]
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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