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In Print: Recent Proteomics Papers of Note: Apr 11, 2014

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In Print: Recent Proteomics Papers of Note

Journal: Molecular & Cellular Proteomics, Feb. 3 [Epub ahead of print]

Title: Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra.

Authors: Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N.

The authors present an approach for improving identification of linked peptides in which they generate large mass spec reference libraries for linked peptides which they then use to train algorithms for identifying these spectra.


Journal: Proteomics, Feb. 12 [Epub ahead of print]

Title: Characterization of individual mouse cerebrospinal fluid proteomes.

Authors: Smith JS, Angel TE, Chavkin C, Orton DJ, Moore RJ, Smith RD.

The authors used 2D-LC MS/MS to analyze mouse cerebrospinal fluid, an approach that had previously been impractical due to the small volume of sample available. They identified 566 proteins, including 128 previously identified in brain tissue.


Journal: Journal of Proteome Research, Feb. 17 [Epub ahead of print]

Title: A chromosome-centric analysis of antibodies directed toward the human proteome using Antibodypedia.

Authors: Alm T, von Feilitzen K, Lundberg E, Sivertsson A, Uhlén M.

The authors used the chromosome-centric Human Proteome Project to benchmark the availability of antibodies to the human proteome, finding that more than 10 antibodies exist to more than 70 percent of putative human genes evenly distributed over the 24 chromosomes and that less than 10 percent of putative human protein-coding genes lack antibodies.


Journal: Nature Cell Biology, Feb. 23 [Epub ahead of print]

Title: Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components.

Authors: Alabert C, Bukowski-Wills JC, Lee SB, Kustatscher G, Nakamura K, de Lima Alves F, Menard P, Mejlvang J, Rappsilber J, Groth A.

The authors used nascent chromosome capture to profile the chromatin proteome during cell replication, identifying factors associated with various parts of the replication process and predicting functions in nascent chromatin for 93 previously uncharacterized proteins.


Journal: Journal of Proteome Research, March 6 [Epub ahead of print]

Title: High-affinity recombinant antibody fragments (Fabs) can be applied in peptide enrichment immuno-MRM assays.

Authors: Whiteaker JR1, Zhao L, Frisch C, Ylera F, Harth S, Knappik A, Paulovich AG.

The authors explored whether high affinity Fabs could be isolated for enrichment of specific peptides, finding that these reagents demonstrated similar performance compared to mouse- or rabbit-derived monoclonal antibodies and as such are suitable for immuno-MRM workflows.


Journal: Journal of Proteome Research, March 11 [Epub ahead of print]

Title: A simple protocol to routinely assess the uniformity of proteomics analyses.

Authors: Gallien S, Bourmaud A, Domon B.

The authors presented a procedure for quality control of mass spec workflows across laboratories by comparing endogenous peptides and their isotopically labeled peptides to monitor bias introduced by sample prep and LC-MS procedures.


Journal: PLOS One, March 11

Title: Detection of viral proteins in human cells lines by xeno-proteomics: elimination of the last valid excuse for not testing every cellular proteome dataset for viral proteins.

Authors: Chernobrovkin AL, Zubarev RA.

The authors present a procedure for untargeted detection of viral protein contaminants in human cell line samples.


Journal: Journal of Proteome Research, March 18 [Epub ahead of print]

Title: Intelligent data acquisition blends targeted and discovery methods.

Authors: Bailey DJ, McDevitt MT, Westphall MS, Pagliarini DJ, Coon JJ.

The authors present an online peptide elution order alignment algorithm that targets peptides based on their relative elution order, allowing researchers to precisely target peptides while also identifying thousands of non-targeted peptides in the same experiment. Applying the method to targeted analysis of 500 mouse peptides, they identified 440, compared to 256 using standard data-dependent acquisition, while also identifying 3,757 other peptides.


Journal: Journal of Proteomics, March 27 [Epub ahead of print]

Title: In-depth proteomic delineation of the colorectal cancer exoproteome: Mechanistic insight and identification of potential biomarkers.

Authors: Karagiannis GS, Pavlou MP, Saraon P, Musrap N, Xie A5, Batruch I, Prassas I, Dimitromanolakis A, Petraki C, Diamandis EP.

The authors used LC-MS/MS to profile the exoproteome of 12 colon cancer cell lines, identifying 2,979 proteins. Additionally, the identified as potentially clinically important proteins including olfactomedin-4 and kallikrein-related peptidases-6 and -10.

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