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Articles tagged: spectral library
Identifying Mycobacteria with custom spectral libraries
Mass spectrometry can be used for rapid identification of difficult to culture or slow growing bacteria so that the patient can receive prompt treatment. The quickest identification method is searching the MS/MS spectra against a species-specific spectral library (SL). Here, we detail the steps to build a custom Mycobacteria spectral library and using it with Mascot Server. Identification of Mycobacteria One [...]
Converting BLIB spectral libraries to MSP (and back again) for use with Mascot Server
Mascot Server can create and search NIST MSP formatted spectral libraries. However, BiblioSpec, which is part of the Skyline software, creates spectral libraries in the BLIB format which cannot be used. We have developed a script that can convert BLIB to MSP files or vice versa, MSP to BLIB files. The conversion script allows Mascot Server to search in silico [...]
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 [...]
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 [...]
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, [...]
X!Hunter MGF libraries
Mascot 2.6 supports three file formats for spectral libraries: the NIST MSP format, the SpectraST sptxt format and the X!Hunter MGF format. The sptxt format is a variation on MSP and will be covered in a future blog post. The main functional difference between MSP and MGF is in the level of annotation. The X!Hunter MGF format is minimalistic and [...]
Don’t wait: use spectral libraries now
The Human Proteome Project 2018 special issue in the Journal of Proteome Research contains a report from the 2017 Dagstuhl Seminar on Computational Proteomics. The paper by Deutsch et al. is titled Expanding the Use of Spectral Libraries in Proteomics, and the authors identify several challenges that slow down spectral library adoption. I’d like to address their main points. Adoption [...]
How to create a spectral library for contaminants
An earlier article highlighted how modified and non-specific peptides from contaminants can be matched using a spectral library without increasing the search space for the target proteins. This is particularly useful for sequencing grade trypsin, which is modified by methylation or acetylation of the lysines, creating a large number of modified non-specific peptides that are missed by typical search strategies. [...]
Exporting spectral library search results
Mascot 2.6 integrates spectral library searching. Today we’ll describe how these searches can be exported. Please ensure you’ve installed the Mascot 2.6.1 patch, as support for exporting library search data was not complete in the initial Mascot 2.6.0 release. Library searches can be either library-only or integrated searches. Integrated means the search is against both a spectral library and a [...]
The most analysed protein is …
Trypsin, of course. The Journal of Proteome Research has a paper from the Medical University of Graz concerning the importance of correctly identifying spectra from contaminant proteins. In particular, trypsin autolysis peptides. The authors point out that sequencing grade trypsin is modified by methylation or acetylation of the lysines, to inhibit autolysis. Unless these variable modifications are selected in a [...]