Welcome

We recently added support for exporting search results as mzIdentML 1.2.

This month's highlighted publication shows an approach to identify biomarkers of residual malaria parasites by analyzing extracellular vesicles. If you have a recent publication that you would like us to consider for an upcoming Newsletter, please send us a PDF or a URL.

Mascot Server 2.8.2 fixes an issue with downloading UniProt proteomes.

Please have a read and feel free to contact us if you have any comments or questions.

Exporting search results as mzIdentML 1.2

Mascot Server 2.8.1 added support for exporting search results as mzIdentML 1.2, which is the latest version of the Proteomics Standards Initiative (PSI) file format. When you export standard database searches, error tolerant searches and spectral library searches, you can choose between mzIdentML 1.1 and 1.2 depending on your requirements.

The new format changes the interpretation of controlled vocabulary terms in specific use cases. The XML structure stays the same, so the new version is otherwise backwards compatible and mostly forwards compatible. There are a few noteworthy changes.

Crosslinked peptides: mzIdentML 1.2 specifies a number of new terms and specific ways of encoding crosslinked peptide matches. All the peptide-level metadata for intact crosslinks have been implemented in Mascot. The file format currently lacks full support for monolinks and looplinks, but these should be added in a future mzIdentML specification.

Protein relationships: Several new terms were introduced for encoding relationships between proteins and protein groups. Only a small change was needed in Mascot for four new terms: cluster identifier, leading protein, group representative and non-leading protein.

Site analysis: mzIdentML 1.2 includes new syntax for encoding site analysis results and modification localization scores. Unfortunately, the syntax is not suitable for Mascot's site analysis, so if you need this, please export the search as mzIdentML 1.1 or as CSV/XML.

Read more about exporting mzIdentML in our blog.

Featured publication using Mascot

Here we highlight a recent interesting and important publication that employs Mascot for protein identification, quantitation, or characterization. If you would like one of your papers highlighted here please send us a PDF or a URL.

Mass spectrometry identification of biomarkers in extracellular vesicles from Plasmodium vivax liver hypnozoite infections

Melisa Gualdrón-López, Miriam Díaz-Varela, Gigliola Zanghi, Iris Aparici-Herraiz, Ryan W.J. Steel, Carola Schäfer, Pol Cuscó, Vorada Chuenchob, Niwat Kangwangransan, Zachary P. Billman, Tayla M. Olsen, Juan R. González, Wanlapa Roobsoong, Jetsumon Sattabongkot, Sean C. Murphy, Sebastian A. Mikolajczak, Eva Borràs, Eduard Sabidó, Carmen Fernandez-Becerra, Erika L. Flannery, Stefan H.I. Kappe, Hernando A. del Portillo

Molecular & Cellular Proteomics, August 24, 2022, in press

The authors searched for potential protein biomarkers that can indicate the presence of liver hypnozoites, which are dormant malaria parasites that can reactivate and cause relapses of malarial disease. Their approach was to generate in vivo infections of P. vivax and explore the protein content of extracellular vesicles (EVs) derived from hypnozoite-infected liver cells.

Five different groups of mice engrafted with human hepatocytes were used in these studies: uninfected control animals, mice infected with P. vivax by mosquito bite, mice infected by intravenous injection and further treated with MMV048 (to stop interfering reproduction), and those treated with the antimalarial Tafenoquine.

Plasma-derived EVs were purified by size exclusion chromatography, digested, and analyzed by LC/MS/MS using DDA. The data were searched against a customized database including P. vivax, Swiss-Prot human and mouse databases. Protein relative quantification was performed using the Abundance Estimated per sample (AEpS), which is calculated as the average areas of the top 3 most abundant peptides per protein.

The enriched SEC fractions contained proteins from the three species: 159 human, 331 mouse and 66 P. vivax. Screening of hypnozoites-specific proteins associated to EVs was done by comparing the protein ratios of P. vivax proteins across the different experimental groups, showing the presence of 13 potential candidate proteins.

Mascot Server 2.8.2

We have released a small patch, Mascot Server 2.8.2, that fixes two bugs related to setting up UniProt proteomes in Database Manager using the new UniProt API; three regressions introduced in version 2.8.1; and one bug with error tolerant top-down searches in cluster mode. If you download UniProt proteomes using Database Manager, we recommend updating. The update is free to download if you have Mascot version 2.8.

Updating from 2.8.0 to 2.8.2 includes all the improvements and fixes from patch 2.8.1. Mascot Server 2.8.1 added mzIdentML 1.2 as an export option, as well as removed an unintended database size limit and greatly improved the compression speed of very large databases like NCBI nr (600+ million protein accessions).

If you have Mascot Server 2.7 or earlier, a workaround for UniProt downloads is documented in our blog. Alternatively, updating costs a fraction of the cost of a new licence. Please contact us if you have any questions.

About Matrix Science

Matrix Science is a provider of bioinformatics tools to proteomics researchers and scientists, enabling the rapid, confident identification and quantitation of proteins. Mascot software products fully support data from mass spectrometry instruments made by Agilent, Bruker, Sciex, Shimadzu, Thermo Scientific, and Waters.

Please contact us or one of our marketing partners for more information on how you can power your proteomics with Mascot.

Matrix Science Ltd, 64 Baker Street, London W1U 7GB, UK
T +44 (0)20 7486 1050  F +44 (0)20 7224 1344  E info@matrixscience.com