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Articles tagged: quantitation
Complementary reporter ion clusters in TMT/TMTpro labeling
We recently received a support request about complementary ions in TMTpro labeling. Complementary ions are formed during fragmentation, where the precursor loses the reporter ion and carbon monoxide, leaving behind the peptide and the balance region of the label. Complementary ion spacing is similar to reporter ions but the mass varies depending on peptide mass. The customer was concerned that [...]
Reporting quantitation datasets with Mascot Distiller 2.8
In previous versions of Distiller, reporting of quantitation results was handled using XSLT transformation of the XML export of the quantitation results. XSLT is a powerful language, but it’s not commonly used, so writing custom reports could be an uphill stuggle. In Mascot Distiller 2.8, reports are written in Python and use Mascot Parser to access the search and quantitation [...]
Divide and conquer: Fractionated Label Free Quantitation in Mascot Distiller 2.8.2
We have recently released Mascot Distiller 2.8.2. The headline new feature is support for Label-Free Quantitation of fractionated samples. With Mascot Distiller 2.8, individual raw files in a project are aligned against a consensus generated by roughly aligning and combining the total ion chromatograms (TICs) of each raw file. If a peptide match is found in one sample file and [...]
Improving precursor quantitation results with ion mobility filtering
One of the major new features in Mascot Distiller 2.8 is support for raw data files from the Bruker timsTOF instrument. timsTOF combines an ion mobility dimension with QTOF, allowing an additional separation dimension. The instrument can use this to help separate MS/MS spectra from otherwise isobaric peptides. Mascot Distiller 2.8 can use the precursor ion mobility values for identified [...]
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 [...]
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 [...]
The three Ds: Diethylation, Dimethylation and the Deuterium effect
Dimethylation Mascot Server and Mascot Distiller support a number of precursor intensity based quantitation techniques using a number of different techniques and chemistries. The software also allows you to flexibly define your own methods, allowing you to implement quantitation protocols which we have not supplied ‘out of the box’. One isotope labelling method which Distiller supports ‘out of the box’ [...]
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 [...]