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In Print: Recent Proteomics Papers of Note: Feb 21, 2014

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In Print: Recent Proteomics Papers of Note

Journal: Journal of Proteome Research, Jan. 14, 2014 [Epub ahead of print]

Title: Assessment of peptide chemical modifications on the development of an accurate and precise multiplex selected reaction monitoring assay for apolipoprotein E isoforms.

Authors: Martínez-Morillo E, Nielsen HM, Batruch I, Drabovich AP, Begcevic I, Lopez MF, Minthon L, Bu G, Mattsson N, Portelius E, Hansson O, Diamandis EP.

The researchers present a mass spec assay for absolute quantification of ApoE isoforms in cerebrospinal fluid and plasma using isotope-labeled peptides. Using the assay, they were able to correctly assign the ApoE phenotype to all samples in a blinded manner.


Journal: Analytical Chemistry, Jan 15, 2014 [Epub ahead of print]

Title: Depletion of abundant plasma proteins by poly(N-isopropylacrylamide-acrylic acid) hydrogel particles.

Authors: Such-Sanmartín G, Ventura-Espejo E, Jensen ON.

The authors present a series of protocols for depletion of high-abundance proteins using hydrogel particles and demonstrated its use for improving detection of a series of protein biomarkers using selected-reaction monitoring mass spec.


Journal: Proceedings of the National Academy of Science, Jan. 21, 2014 [Epub ahead of print]

Title: Digital microfluidic assay for protein detection.

Authors: Mok J, Mindrinos MN, Davis RW, Javanmard M.

The authors present a low-cost, digital microfluidic platform for protein biomarker detection that makes use of simple electronics, allowing for potential translation into a portable handheld device. The demonstrated it by detecting interleukin-6 in concentrations as low as 50 picomoles in less than 5 μL of sample, and Abelson tyrosine kinase activity in samples containing 100 picomoles of kinase.


Journal: Analytical Chemistry, Jan. 21, 2014 [Epub ahead of print]

Title: Dual matrix-based immobilized trypsin for complementary proteolytic digestion and fast proteomics analysis with higher protein sequence coverage.

Authors: Fan C, Shi Z, Pan Y, Song Z, Zhang W, Zhao X, Tian F, Peng B, Qin W, Cai Y, Qian X.

The authors present a dual matrix-based complementary digestion method using two forms of immobilized trypsin with opposite matrix hydrophobicity, leading to improvements in the speed and efficiency of protein digestion.


Journal: Analytical Chemistry, Jan 23, 2014 [Epub ahead of print]

Title: Autopilot: an online data acquisition control system for the enhanced high-throughput characterization of intact proteins.

Authors: Durbin KR, Fellers RT, Ntai I, Kelleher NL, Compton PD.

The authors present a new software package for acquisition of top-down proteomics data that allows for fully automated detection of intact masses, guiding of fragmentation, and database searching to enable real-time protein identifications. Applying the software to Pseudomonas aeruginosa they achieved improved characterization of their targets by an average of 42 orders of magnitude in confidence.


Journal: Cell Reports, Jan 23, 2014 Epub ahead of print]

Title: Specificity and commonality of the phosphoinositide-binding proteome analyzed by quantitative mass spectrometry.

Authors: Jungmichel S, Sylvestersen KB, Choudhary C, Nguyen S, Mann M, Nielsen ML.

The authors used mass spec analysis to identify phosphoinositide-interacting proteins and profile their binding specificities, identifying 405 such proteins, which, they noted in the abstract "is greater than the total number of phospho- or ubiquitin-binding domains.


Journal: Alzheimer's & Dementia, Jan 2014

Title: Developing novel blood-based biomarkers for Alzheimer's disease.

Authors: Snyder HM, Carrillo MC, Grodstein F, Henriksen K, Jeromin A, Lovestone S, Mielke MM, O'Bryant S, Sarasa M, Sjøgren M, Soares H, Teeling J, Trushina E, Ward M, West T, Bain LJ, Shineman DW, Weiner M, Fillit HM.

The authors present a summary of a meeting arranged by the Alzheimer's Association and the Alzheimer's Drug Discovery Foundation to bring top Alzheimer's scientists together, giving an overview of the state of blood-based biomarker development in the field.


Journal: Journal of Proteome Research, Feb. 11, 2014 [Epub ahead of print]

Title: Using mass spectrometry to monitor monoclonal immunoglobulins in patients with a monoclonal gammopathy.

Authors: Barnidge DR, Dasari S, Botz CM, Murray DH, Snyder MR, Katzmann JA, Dispenzieri A, Murray DL.

The authors used mass spec to detect and quantify monoclonal immunoglobulin (M-protein) to detect monoclonal gammopathy. Enriching serum for immunoglobulins, they then analyzed their sample using LC-ESI-QTOF mass spec, demonstrating the ability to pick up M-protein in multiple myeloma samples that were negative for the protein according to protein gel electrophoresis, immunofixation electrophoresis, and quantitative FLC.

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