Advances in Tools to Determine the Glycan-Binding Specificities of Lectins and Antibodies

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Highlights

• •Lectins and glycan-binding antibodies are valuable as probe of glycans.
• •Advanced bioinformatics tools enable the mining of glycan-array data.
• •New insights into protein-glycan interactions have value in biological research.

     

MSstatsTMT: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures

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Highlights

• •Statistical approach for differential abundance analysis for proteomic experiments with TMT labeling.
• •Applicable to large-scale experiments with complex or unbalanced design.
• •An open-source R/Bioconductor package compatible with popular data processing tools.

     

MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics

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Highlights

• •Highly parallelizable 4D feature detection in ion mobility enhanced shotgun proteomics.
• •Multidimensional non-linear mass, retention time and ion mobility recalibration.
• •Collision cross section aware matching between runs.
• •Label-free quantification of ion mobility MS data.

     

Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks

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Highlights

• •Co-elution stands out as a global interactome mapping method.
• •Benefits include all-to-all protein analysis and measurement of interactome perturbations.
• •Different separation, quantification and bioinformatic strategies are available.
• •Design considerations depend largely on system under study.

     

Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments

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Highlights

• •Automated statistical approach for detecting uninformative features and outliers.
• •Improved performance on relative protein quantification.
• •An option in the open-source R-based software MSstats.

     

Examining and Fine-tuning the Selection of Glycan Compositions with GlyConnect Compozitor

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Highlights

• •New comparative tool to assess the relevance of a glycan composition file to be used in a glycoproteomic study.
• •User-friendly and web-based interface to explore glycoproteomics data.
• •Detection of glycan compositional trends within and across protein(s) or tissues.

     

Peptidomic Analysis of Urine from Youths with Early Type 1 Diabetes Reveals Novel Bioactivity of Uromodulin Peptides In Vitro

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Highlights

• •Urinary peptide profiling of youths with type 1 diabetes before clinical injury.
• •Internal validation of uromodulin peptides by parallel reaction monitoring.
• •Discovery of novel bioactivity of uromodulin peptides in vitro.
• •In silico prediction of proteases involved in uromodulin processing.

     

Identification of Lysine Acetylation Sites on MERS-CoV Replicase pp1ab

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Highlights

• •Acetylation sites on MERS-CoV protein pp1ab were reported for the first time.
• •Sirt1 was predicted as upstream factor of identified acetylation events.

     

Genetic Profile and Functional Proteomics of Anal Squamous Cell Carcinoma: Proposal for a Molecular Classification

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Highlights

• •Two molecular groups in anal squamous carcinoma according proteomic profile.
• •Differences in possible targeted processes such as metabolism or immune response.
• •Different percentage of tumor lymphocyte infiltration.
• •Difference in the frequency of ATM variants, related to PPAR inhibitors.

     

Immediate Adaptation Analysis Implicates BCL6 as an EGFR-TKI Combination Therapy Target in NSCLC

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Highlights

• •EGFR-TKI molecular response profiling covering 10138 proteins and 13486 mRNAs.
• •EGFR-TKI combination therapy screen using a library of 528 compounds.
• •Several new candidate EGFR-TKI escape mechanisms and combination therapy targets.
• •Combined targeting of the oncogene BCL6 and EGFR results in synergy in NSCLC cells.

     

Characterization of Prenylated C-terminal Peptides Using a Thiopropyl-based Capture Technique and LC-MS/MS

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Highlights

• •Brain membrane protein extraction.
• •Protein prenylation.
• •Prenyl peptide capture and characterization by LC-MS/MS.
• •HCD and EThcD peptide fragmentation.

     

Measuring Site-specific Glycosylation Similarity between Influenza a Virus Variants with Statistical Certainty

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Highlights

• •Changes in N-linked glycosylation in influenza A virus affect antigenicity of the virus.
• •Glycosylation similarity can be quantified, even in heterogeneously glycosylated proteins.
• •Glycosylation is measurably and site-specifically distinct in influenza from related strains.

     

Open Database Searching Enables the Identification and Comparison of Bacterial Glycoproteomes without Defining Glycan Compositions Prior to Searching

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Highlights

• •We demonstrate the use of open searching for the detection of atypical glycosylation in bacterial glycoproteomes.
• •We show that although open searching is able to detect unique glycoforms it is less sensitive for the detection of multiply glycosylated peptides than focused searches.
• •Using open search delta mass profiles, we demonstrate glycan use across bacterial glycoproteomes can be easily compared.
• •For the Burkholderia genus we confirm the use of similar glycans for protein glycosylation yet also highlight that species specific glycans do exist.

     

Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes

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Highlights

• •Guidelines for studying protein complexes via co-fractionation mass spectrometry.
• •A novel procedure for profiling gold standard protein complexes in CF-MS data.
• •Recommendations for efficient CF-MS fractionation collection.
• •Scoring metric recommendations for precise and sensitive CF-MS data analysis.

     

Developments and Applications of Functional Protein Microarrays

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Highlights

• •Summarize the development of functional protein microarray.
• •Application of functional proteome microarray in basic research.
• •Application of functional proteome microarray in translational research.
• •Fabrication of functional membrane protein array using virion display method.

     

DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis

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Highlights

• •DEqMS is a method for statistical analysis of quantitative MS-data.
• •Variance estimates based on the actual MS-data structure.
• •Improved statistical power and accuracy in protein differential analysis.
• •DEqMS is available as a user-friendly R package in Bioconductor.

     

Proteomic Analysis Reveals that Topoisomerase 2A is Associated with Defective Sperm Head Morphology

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Highlights

• •Human spermatozoa possess cells of poor morphology that lack nuclear integrity.
• •These cells can be isolated by density separation.
• •Mass spectrometry reveals their nuclei contain excess protein.
• •TOP2A is a promising marker of this poor nuclear development.

     

Seminal Plasma Proteome as an Indicator of Sperm Dysfunction and Low Sperm Motility in Chickens

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Highlights

• •Quantitative proteomes of chicken seminal plasma associated with sperm motility.
• •High abundant acrosome and mitochondrial proteins were noted in LSM seminal plasma.
• •Decreased total antioxidant capacity was highlighted in seminal plasma of LSM.
• •Lack of membrane, acrosome and mitochondrial integrity and high ROS may induce LSM.