Blog
How old is the software in that publication?
Most proteomics data analysis requires complex and sophisticated software. When you read the methods section of a journal article, it should state the software name and version number, as this is the minimum required for reproducibility of the data analysis. Often it is useful to also know how old the software package is. If it’s Mascot Server, there is now [...]
Get more search speed with SplitNumberOfQueries
Mascot Server has several parameters and options that have an effect on database search duration. One of them is SplitNumberOfQueries, which specifies how many queries (MS/MS spectra) are searched at a time. The default is 1000 queries, which is reasonable, but like all defaults, it isn’t optimal. On most hardware, increasing it to 2000 will yield an immediate 10-20% performance [...]
Generating high quality spectral libraries for DIA-MS
Using Mascot Daemon, Mascot Distiller and Mascot Server A recent paper from Manda et al.[1] describes a pipeline to generate high quality spectral libraries from Data-Dependent Acquisition (DDA) experiments for use in searching Data-Independent Acquisition (DIA) data, starting from the raw data, through to generating the library from the search results. The pipeline uses a collection of different tools in [...]
25 years of Matrix Science
Happy 25th birthday, Matrix Science! A lot has happened since John Cottrell and David Creasy founded the company in 1998, and proteomics today certainly looks very different to the bleeding edge of science back then. The success of any company could be attributed to various causes, but the simple fact is that we would not be here without our loyal [...]
Mascot in the Cloud
Cloud computing is the IT paradigm of our times. More and more business services and applications are delivered as a subscription service, where the software runs in a data centre somewhere, operated by a third-party cloud platform. We are often asked whether you can run Mascot Server “in the cloud” and if so, whether it’s the right solution. The answers [...]
Peak picking intact crosslink spectra with Mascot Distiller
There are several important factors to take into account when carrying out peakpicking for an intact crosslinked dataset. You’ll typically be dealing with higher charge state precursors to handle the larger masses of the linked peptides, and the MS/MS spectra are inherently complex, chimeric spectra with fragments from the alpha and beta peptides. To look at the effects of adjusting [...]
Paleoproteomics
Paleoproteomics is a growing application area for mass spectrometry. Its cross-disciplinary remit includes analysis of ancient proteins (bone, skin, silk), ancient proteomes (enamel, egg shells, plant seeds) and most ambitiously ancient metaproteomes (dental calculus, food remains). The recent review by Warinner et al. in Chemical Reviews has excellent coverage not just of the varied applications but also the sample processing [...]
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 [...]
Downloading UniProt proteomes via new API
The UniProt website received a snazzy facelift in June 2022. Both the browser interface and the REST API were updated. The previous version, now termed legacy website, remains available until the 2022_04 release under a new URL (https://legacy.uniprot.org/) – so there is limited time to compare and admire the improvements! The new API is an almost seamless transition for Mascot [...]
Does your search engine show the evidence?
You’ve submitted a protein sequence database search and start looking at the results. Why did the search engine identify that protein? What is the peptide evidence? Which alternatives did the software consider? Is the software’s decision correct? These are basic yet important questions with any software-driven approach – which is the bulk of today’s MS/MS data analysis. A lot of [...]
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 [...]
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