Blog
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 [...]
mzIdentML 1.2
Mascot Server supports several formats for exporting database search results. One of them is the Proteomics Standards Initiative’s mzIdentML. The Mascot 2.8.1 patch release upgrades the file format version to mzIdentML 1.2. You can now export crosslinked search results in XML, CSV, xiVIEW CSV and mzIdentML format. When you export standard database searches, error tolerant searches and spectral library searches, [...]
NCBI nr in Mascot Server 2.8.1
Mascot Server 2.8.01 patch was released in March 2022. One of the big improvements is optimising the compression speed of the NCBI nr database, available as the NCBIprot predefined definition. We’ve greatly decreased the time it takes to bring the database online, as well as removed an inadvertent limitation on database size. The patch is available to download on the [...]
Analyzing the disulfide bond structure of the SARS-Cov-2 Spike protein
The SARS-Cov-2 virus has been under intense investigation since its discovery two years ago. Almost every feasible analytical method has been used and according to PubMed, that includes over 3000 proteomics papers. The most important protein immunologically speaking is the spike protein that is involved in the initial binding to the target cells. An example of the more encompassing spike [...]
Single-cell peptide fragmentation spectra
More single-cell proteomics studies are published each year as instruments become more sensitive and sample preparation is optimised. A recent publication in the Journal of Proteome Research, Features of Peptide Fragmentation Spectra in Single-Cell Proteomics, highlights potential challenges to protein and peptide identification by database searching. Boekweg et al. computationally examined the fragmentation spectra of peptides from bulk samples, 2ng [...]
Default or prof_prof? Peak picking Thermo .RAW data with Mascot Distiller
We supply a number of processing options files for each of the main vendor raw file types with Mascot Distiller. These .opt files are designed as a reasonable starting point for peak picking your own data – but to get the very best you’ll need to tweak the parameters on a typical raw file from your instruments and then use [...]
Mascot cluster installation security on Linux
Mascot Server has a built-in cluster mode, where the database search can be executed in parallel on a networked cluster of PCs. This requires no special hardware or operating software. The cluster can consist of ‘commodity’ PCs running Windows or Linux. Cluster mode is usually the most practical option for licences of 5 CPU or more, as discussed in Mascot [...]
Retiring the File Transfer Protocol (FTP)
Mascot Server includes Database Manager, which can be configured to download protein sequence databases from many sources using FTP (File Transfer Protocol), HTTP (Hyper Text Transfer Protocol) and HTTPS (HTTP Secure). FTP is the oldest of these protocols by far, making its first appearance in 1971. Until some years ago, FTP was the best and only choice for large file [...]
Choosing hardware for Mascot Distiller
One question which comes up frequently with regards to Mascot Distiller is what is a good specification for the workstation it’s going to be installed on. By that, we’re really interested in what sort of CPU you should be getting, how much RAM the workstation should have, and what sort of disk drives (SSD or HDD) should you be getting. [...]
Identify more HLA peptides
Endogenous peptides are challenging to identify by database searching. A Mascot no-enzyme search matches every subsequence of a protein to the observed spectrum, which makes a very large search space even if precursor tolerance is tight. As a result, Mascot score thresholds tend to be conservative and sensitivity is reduced. Mascot ships with Percolator, which often improves discrimination between true [...]
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