Blog
Articles tagged: error tolerant
Matrix Science at ASMS 2024
The ASMS 2024 conference was held in Anaheim, California, on 2-6 June 2024. It was great to see many of you at our booth as well as the annual Breakfast Meeting! We presented three talks at the meeting. If you were unable to attend, or want to review any of the material that was presented, the talks are summarised below [...]
30 years of Sequence Tags
This year we are celebrating 30 years of sequence tags. The technique was developed by Matthias Mann and Matthias Wilm while in the Protein and Peptide group at the European Molecular Biology Laboratory (EMBL). EMBL is itself celebrating its 50th Anniversary and has been an important center for science over that period. The sequence tag paper was published in 1994, [...]
Finding unsuspected modifications in narrow-window DIA data using the Mascot Error Tolerant Search
Mascot’s spectrum-centric approach doesn’t have the constraints on variable modifications, missed cleavages and protein sequences that are required by peptide-centric DIA tools. In fact, it’s nearly trivial to identify unsuspected variable modifications in narrow-window DIA data using the Mascot Error Tolerant Search. There can be many reasons for failing to get a significant sequence match to an MS/MS spectrum. Three [...]
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 [...]
Error tolerant searches now show statistical significance
The latest release of Mascot Server introduces some important changes to error tolerant searches. Matches from the second pass search now have expect values attached, indicating confidence levels. These are either estimates based on counting trials or empirical values derived from searching a decoy database. If you are not familiar with the error tolerant search, now is the time to [...]
Variable Modifications in Mascot 2.7
Most protein samples will exhibit some degree of modification which needs to be considered when carrying out a database search In this article we’ll take a look at some important changes we introduced in Mascot 2.7 in how Mascot handles variable modifications. Variable modification permutation in Mascot 2.6 and earlier In Mascot 2.6 or earlier, variable modification permutation is handled [...]
The plus one dilemma
There are several common modifications that can add approximately 1 Da to a peptide mass. Even if you have high accuracy data, it can sometimes be difficult to figure out which one is correct. Delta Lys->Glu substitution 0.947630 Leu->Asn or Ile->Asn substitution 0.958863 Deamidation at N or Asn->Asp substitution 0.984016 Deamidation at Q or Gln->Glu substitution 0.984016 Citrullination at [...]
Back to Basics: Optimize your search parameters
Every now and then you need to determine good search parameters for a data set. They may be different from the normal ones you use due to a change in instrumentation, you may be analyzing data from a public resource like PRIDE/Proteome exchange or it could be data from a collaborator. Whatever the reason, here’s a quick overview on how [...]
Results round-up for the ‘dark matter’ challenge
In June, we tried to harness the power of crowd-sourcing to explain some of the unidentified modifications found in open database searches. We selected 20 abundant and unassigned mass deltas from Supplementary Table 3 of the recent MSFragger paper from Alexey Nesvizhskii’s group at U. Michigan and offered prizes for the first credible explanations. There were 35 unannotated deltas in [...]
Step away from the iodoacetamide
In our July newsletter, we featured a paper from Torsten Müller and Dominic Winter, University of Bonn, concerning alkylation artefacts. Some of their findings were quite shocking. For example, differences of more than 9 fold in numbers of identified methionine-containing peptides for in-gel digested samples between iodine- and non-iodine-containing alkylation reagents. This is important because a glance at the literature [...]