Pursuing Impactful Quantitative Proteomics Using QC-Channels in Every Spectrum and Trend-Design in Experiment

False changes discovered by quantitative proteomics reduce the trust of biologists in proteomics and limit the applications of proteomics to unlock biological mechanisms, which suppresses the application of proteomics techniques in the pharmaceutical industry more than it does in academic research. To remove false changes that arise during LC-MS/MS data acquisition, we evaluated the contributions of peptide abundance and number of unique peptides on reproducibility. Lower abundance and only one unique peptide have a higher risk of generating a higher coefficient of variation (CV), resulting in less accurate quantification. However, the abundance of peptides in samples is not adjustable and discarding proteins quantified by only one unique peptide is not a choice either. Indeed, a large percentage of proteins are accurately quantified by only one unique peptide. Therefore, to improve the calculations of the CV, we leverage a new function in PEAKS called QC-channels which enables technical replicates of each spectrum to be evaluated prior to calculation of the CV. While the QC-channels function in PEAKS significantly reduced the false quantification, random false changes still exist due to known or unknown reasons. To address this challenge, we present the idea of Trend-design to track trend changes rather than changes from two points to remove false quantifications and reveal consequential changes responding to a treatment or condition. The idea was confirmed by molecules with different affinity and dose in the current study. The combination of QC-channels and Trend-design enables a more impactful quantitative proteomics to allow unlocking biological mechanisms using proteomics.

Speech assessment following microsurgical soft palate repair

The aim of this study was to analyze speech intelligibility of children, who had undergone microsurgical soft palate repair according to Sommerlad. Cleft palate patients were treated by closure of the soft palate according to Sommerlad at about 6 months of age. At the age of 11, their speech was evaluated through automatic speech recognition. Word recognition rate (WR) was used as the outcome parameter of automatic speech recognition. To validate automatic speech results, an institute for speech therapy evaluated the speech samples for perceptual intelligibility. The results of this study group were compared to an age-matched control group. A total of 61 children were evaluated in this study, 29 in the study group and 32 in the control group. Study group patients had a lower word recognition rate (mean 43.03, SD 12.31) compared to the control group (mean 49.98, SD 12.54, p = 0.033). The magnitude of the difference was considered small (95% CI of the difference 0.6-13.3). The study group patients received significantly lower scores in the perceptual evaluation (mean 1.82, SD 0.58) compared to the control group mean (mean 1.51, SD 0.48, p = 0.028). Again, the magnitude of the difference was small (95% CI of the difference 0.03-0.57). Within the limitations of the study it seems that microsurgical soft palate repair according to Sommerlad at the age of 6 months might be a relevant alternative to other well established surgical techniques.

Database search engines and target database features impinge upon the identification of post-translationally cis-spliced peptides in HLA class I immunopeptidomes

Unconventional epitopes presented by HLA class I complexes are emerging targets for T cell targeted immunotherapies. Their identification by mass spectrometry (MS) required development of novel methods to cope with the large number of theoretical candidates. Methods to identify post-translationally spliced peptides led to a broad range of outcomes. We here investigated the impact of three common database search engines - that is, Mascot, Mascot+Percolator, and PEAKS DB - as final identification step, as well as the features of target database on the ability to correctly identify non-spliced and cis-spliced peptides. We used ground truth datasets measured by MS to benchmark methods' performance and extended the analysis to HLA class I immunopeptidomes. PEAKS DB showed better precision and recall of cis-spliced peptides and larger number of identified peptides in HLA class I immunopeptidomes than the other search engine strategies. The better performance of PEAKS DB appears to result from better discrimination between target and decoy hits and hence a more robust FDR estimation, and seems independent to peptide and spectrum features here investigated.

Identification of Non-Canonical Translation Products in C. elegans Using Tandem Mass Spectrometry

Transcriptome and ribosome sequencing have revealed the existence of many non-canonical transcripts, mainly containing splice variants, ncRNA, sORFs and altORFs. However, identification and characterization of products that may be translated out of these remains a challenge. Addressing this, we here report on 552 non-canonical proteins and splice variants in the model organism C. elegans using tandem mass spectrometry. Aided by sequencing-based prediction, we generated a custom proteome database tailored to search for non-canonical translation products of C. elegans. Using this database, we mined available mass spectrometric resources of C. elegans, from which 51 novel, non-canonical proteins could be identified. Furthermore, we utilized diverse proteomic and peptidomic strategies to detect 40 novel non-canonical proteins in C. elegans by LC-TIMS-MS/MS, of which 6 were common with our meta-analysis of existing resources. Together, this permits us to provide a resource with detailed annotation of 467 splice variants and 85 novel proteins mapped onto UTRs, non-coding regions and alternative open reading frames of the C. elegans genome.

Speech intelligibility in patients with oral cancer: An objective baseline evaluation of pretreatment function and impairment

BACKGROUND

This study seeks to identify those factors that influence the pre-therapeutic speech intelligibility in patients with oral squamous cell carcinoma (OSCC).

METHOD

A group of 172 patients (125 males, 47 females, mean age = 61 ± 11 a) with different OSCC stages ranging from T1 to T4 and N0 to N2 was examined for their speech intelligibility using a computerized measuring tool, and compared to a healthy reference group (30 males, 10 females, mean age = 59 ± 12 a).

RESULTS

It was found that the pre-therapeutic speech intelligibility in patients with OSCC is decreased when compared to a healthy collective. Two demographic factors that influence speech intelligibility could be identified: sex and age. It was determined that the only disease-related factor that influences speech intelligibility before therapy is the location of the tumor.

CONCLUSION

The results of this study reveal that a preoperative speech intelligibility impairment in patients suffering from OSCC occurs independent of tumor stage, size of the tumor and infiltration status.