A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics

Multiplex proteomics using isobaric labeling tags has emerged as a powerful tool for the simultaneous relative quantification of peptides and proteins across multiple experimental conditions. However, the quantitative accuracy of the approach is largely compromised by ion interference, a phenomenon that causes fold changes to appear compressed. The degree of compression is generally unknown, and the contributing factors are poorly understood. In this study, we thoroughly characterized ion interference at the MS2 level using a defined two-proteome experimental system with known ground-truth. We discovered remarkably poor agreement between the apparent precursor purity in the isolation window and the actual level of observed reporter ion interference in MS2 scans-a discrepancy that we found resolved by considering cofragmentation of peptide ions hidden within the spectral "noise" of the MS1 isolation window. To address this issue, we developed a regression modeling strategy to accurately predict reporter ion interference in any dataset. Finally, we demonstrate the utility of our procedure for improved fold change estimation and unbiased PTM site-to-protein normalization. All computational tools and code required to apply this method to any MS2 TMT dataset are documented and freely available.

Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows

Cross-linking mass spectrometry has matured to a frequently used tool for the investigation of protein structures as well as interactome studies up to a system-wide level. The growing community generated a broad spectrum of applications, linker types, acquisition strategies and specialized data analysis tools, which makes it challenging to decide for an appropriate analysis workflow. Here, we report a large and flexible synthetic peptide library as reliable instrument to benchmark crosslink workflows. Additionally, we provide a tool, IMP-X-FDR, that calculates the real, experimentally validated, FDR, compares results across search engine platforms and analyses crosslink properties in an automated manner. We apply the library with 6 commonly used linker reagents and analyse the data with 6 established search engines. We thereby show that the correct algorithm and search setting choice is highly important to improve identification rate and reliability. We reach identification rates of up to ~70 % of the theoretical maximum (i.e. 700 unique lysine-lysine cross-links) while maintaining a real false-discovery-rate of <3 % at cross-link level with high reproducibility, representatively showing that our test system delivers valuable and statistically solid results.

Cross-linking mass spectrometry is widely used to elucidate protein structures and interactions. Here, the authors generate an extensive peptide library to benchmark the most common cross-link search engines with frequently used cross-linking reagents in low and high complex sample systems.

Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins

Label-free quantification has become a common-practice in many mass spectrometry-based proteomics experiments. In recent years, we and others have shown that spectral clustering can considerably improve the analysis of (primarily large-scale) proteomics data sets. Here we show that spectral clustering can be used to infer additional peptide-spectrum matches and improve the quality of label-free quantitative proteomics data in data sets also containing only tens of MS runs. We analyzed four well-known public benchmark data sets that represent different experimental settings using spectral counting and peak intensity based label-free quantification. In both approaches, the additionally inferred peptide-spectrum matches through our spectra-cluster algorithm improved the detectability of low abundant proteins while increasing the accuracy of the derived quantitative data, without increasing the data sets' noise. Additionally, we developed a Proteome Discoverer node for our spectra-cluster algorithm which allows anyone to rebuild our proposed pipeline using the free version of Proteome Discoverer.

apQuant: Accurate Label-Free Quantification by Quality Filtering

Label-free quantification of shotgun proteomics data is a frequently used strategy, offering high dynamic range, sensitivity, and the ability to compare a high number of samples without additional labeling effort. Here, we present a bioinformatics approach that significantly improves label-free quantification results. We employ Percolator to assess the quality of quantified peptides. This allows to extract accurate and reliable quantitative results based on false discovery rate. Benchmarking our approach on previously published public data shows that it considerably outperforms currently available algorithms. apQuant is available free of charge as a node for Proteome Discoverer.

Phosphoproteomics with Activated Ion Electron Transfer Dissociation

The ability to localize phosphosites to specific amino acid residues is crucial to translating phosphoproteomic data into biological meaningful contexts. In a companion manuscript ( Anal. Chem. 2017 , DOI: 10.1021/acs.analchem.7b00213 ), we described a new implementation of activated ion electron transfer dissociation (AI-ETD) on a quadrupole-Orbitrap-linear ion trap hybrid MS system (Orbitrap Fusion Lumos), which greatly improved peptide fragmentation and identification over ETD and other supplemental activation methods. Here we present the performance of AI-ETD for identifying and localizing sites of phosphorylation in both phosphopeptides and intact phosphoproteins. Using 90 min analyses we show that AI-ETD can identify 24,503 localized phosphopeptide spectral matches enriched from mouse brain lysates, which more than triples identifications from standard ETD experiments and outperforms ETcaD and EThcD as well. AI-ETD achieves these gains through improved quality of fragmentation and MS/MS success rates for all precursor charge states, especially for doubly protonated species. We also evaluate the degree to which phosphate neutral loss occurs from phosphopeptide product ions due to the infrared photoactivation of AI-ETD and show that modifying phosphoRS (a phosphosite localization algorithm) to include phosphate neutral losses can significantly improve localization in AI-ETD spectra. Finally, we demonstrate the utility of AI-ETD in localizing phosphosites in α-casein, an ∼23.5 kDa phosphoprotein that showed eight of nine known phosphorylation sites occupied upon intact mass analysis. AI-ETD provided the greatest sequence coverage for all five charge states investigated and was the only fragmentation method to localize all eight phosphosites for each precursor. Overall, this work highlights the analytical value AI-ETD can bring to both bottom-up and top-down phosphoproteomics.

Mechanical thrombectomy using the Rotarex catheter in the treatment of acute and subacute occlusions of peripheral arteries: immedite results, long-term follow-up

AIM

The aim of this paper was to evaluate the immediate and long-term results of mechanical thrombectomy using the Rotarex catheter in the treatment of acute and subacute occlusions of peripheral arteries.

METHODS

Patients with acute or subacute occlusions of peripheral arteries were selected consecutively for treatment with the Rotarex system. The average age of our patients was 44-92 years (median [m] 75 years). The duration of symptoms ranged from 1 to 90 days (m 14 days).

RESULTS

Seventy-three interventions in 65 patients were performed. Occlusion length varied from 1 to 37 cm (m 10 cm). Immediate successful recanalization was achieved in 69 interventions (95%). Peripheral embolization represented the most frequent transitory complication (6%). Acute reocclusion following 69 successful interventions occurred in a total of 7 procedures (10%). Cumulative patency rates were 56% after 6 months, 47% after 12 months, 41% after 18 months, 37% after 24 months, 33% after 30 months and 29% after 36 months. The ankle/brachial pressure index prior to intervention ranged from 0 to 0.83 (m 0.53) and increased to 0.42-1.44 (m 0.9) post intervention (P<0.001). Its values after 6, 12, 18, 24, 30 and 36 months were statistically significantly higher than those before procedure. Major amputation was performed in 10% of cases.

CONCLUSIONS

Rotarex thrombectomy represents an effective and safe modality for treating acute and subacute occlusions of peripheral arteries with excellent immediate and satisfactory long-term results. Compared to thrombolysis, the principal advantage of thrombectomy is the rapid recanalization of the given artery.

Mechanical thrombectomy using the Rotarex catheter--safe and effective method in the treatment of peripheral arterial thromboembolic occlusions

BACKGROUND

The aim of the study was to evaluate the efficacy of mechanical thrombectomy using the Rotarex catheter in the treatment of peripheral arterial thromboembolic occlusions and to assess long-term results.

PATIENTS AND METHODS

The Rotarex catheter is a 6F or 8F polyurethane catheter, which contains a steel spiral powered by an electric motor and rotating at a speed of 40.000 rpm. The catheter tip is connected to the spiral. The rotating spiral produces a continuous vacuum and the thromboembolic material "drilled" by the tip is drawn into the catheter, where it is fragmented and transported via the spiral to the collecting bag.

RESULTS

We have conducted 43 interventions in 40 patients (20 men, 20 women), age 44-92 years (mean 76 years). The occlusion length varied from 2-37 cm (mean 8 cm); the duration of symptoms ranged from 2-180 days (mean 14 days), Thrombectomy as the only procedure was sufficient in 11 interventions (25.5%); a combination with PTA was necessary in 21 procedures (49%) and with stent implantation in 11 procedures (25.5%). Angiographic success was achieved in 41 interventions (95%). The most frequent transitory complication was embolization to the calf arteries (9%). Subsequent thrombolysis was administered after 4 procedures (9%). In one case (2%) there was a minor perforation of the peroneal artery. Six-month post-intervention follow-up is available for 34 patients. Patency was preserved in 65% and amputation had to be performed in 12%. After 12 months, 12 patients are followed and 67% of interventions have remained patent.

CONCLUSIONS

The Rotarex system enables fast and efficient treatment of peripheral arterial thromboembolic occlusions. In most cases, this method is capable of replacing thrombolysis.