We describe a new statistical scorer for tandem mass spectrometry. The scorer is based on the probability that fragments with given chemical properties create measured intensity levels in the experimental spectrum. The scorer's parameters are computed using a fully automated procedure. Benchmarking the new scorer on a large set of experimental spectra, we show that it performs significantly better than the widely used cross-correlation scoring algorithm of Eng et al. (Eng, J. K; McKormack, A. L.; Yates, J. R. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.).

Objectives To study the effect of repeated retinal thickness fluctuations during the anti-VEGF therapy maintenance phase in neovascular age-related macular degeneration (nAMD). Methods Data were extracted from electronic medical records of 381 nAMD patients, aged ≥50 years; baseline VA ≥33 and ≤73 letters; ≥24 months’ follow-up and ≥2 optical coherence tomography (OCT) measurements. OCT scans were analysed using an artificial intelligence algorithm that quantified the volumes of intraretinal fluid (IRF), subretinal fluid (SRF), pigment epithelial detachments (PED) and central subfield thickness (CSFT). IRF, SRF and PED were summed to obtain total fluid (TF). The standard deviation (SD) of IRF, SRF, PED, CSFT and TF was computed and categorised into quartiles (SD-Q). Relationships between SD-Qs for each OCT feature and VA change was tested using generalised estimating equations and linear regression. Results By Month 24, compared to SD-Q1, eyes in SD-Q2, SD-Q3, and SD-Q4 for IRF, SRF, PED, CSFT and TF showed greater VA losses. Eyes in SD-Q4 of TF were 9.4 letters worse compared to eyes in Q1 (95% Confidence Interval: −12.9 to −6.0). The frequency of clinic visits with IRF and SRF present on OCT scans by quartiles of CSFT was lower in eyes with least fluctuation (Q1) compared to eyes with the most fluid fluctuation (Q4) (median [IQR] IRF: 0.3 [0.0–0.7] versus 0.8 [0.5–1.0]; SRF: 0.0 [0.0–0.5] versus 0.6 [0.3–1.0]). Conclusions Greater fluctuations in retinal fluid volumes during the maintenance phase of anti-VEGF treatment in nAMD is associated with worse VA by 2 years.

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TwinPeaks, a close variant of the SEQUEST protein identification algorithm, is capable of unrestricted, large-scale, identification of post-translation modifications (PTMs). TwinPeaks is applied on a sample of 100441 tandem mass spectra from the HUPO Plasma Proteome Project data set, with full non-redundant human as a reference protein database. With a 3.5% error rate, TwinPeaks identifies a collection of 539 spectra that were not identified by the usual PTM-restricted identification algorithm. At this error rate, TwinPeaks increases the rate of spectra identifications by at least 17.6%, making unrestricted PTM identification an integral part of proteomics.