Tuesday, 1 October 2013

Celebrating Ten Years of Mann and Aebersold’s “Mass spectrometry-based proteomics” review.

In 2003 Mann & Aebersold reviewed on the pages of Nature the challenges and perspectives of the then-nascent field of MS-based proteomics. Mass spectrometry (MS) has since entrenched itself as the method of choice for analyzing complex protein samples, and MS-based proteomics has become an indispensable technology for interpreting genomic data and performing protein analyses (primary sequence, post-translational modifications (PTMs) or protein–protein interactions).

" The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine."
The manuscript by Mann & Aebersold is one of the most cited manuscripts in the field of MS proteomics, For this reason is one of the “core papers” in the field of proteomics and computational proteomics, outlining most of the basic concepts required to understand the fundamentals of this discipline.

Ten years after its publication the main workflow described in the manuscript do not change dramatically. In this period major advances are related to the development of the Thermo’s Orbitrap Mass Spectrometer (Velos, LTQ, Exactive, etc) and new fragmentations types (ETD, HCD). Separation techniques (electrophoretic and chromatographic) were explored extensively in these ten years. Aebersold pioneered in 2005 the use of OFFGEL electrophoresis and electrophoresis fragmentation at peptide level (Heller 2005) and Mann’s group developed the FASP method for sample preparation before protein digestion (Wiśniewski JR et al 2009),both of which have contributed significantly to the dramatic increase in the number of identified proteins characterizing today’s proteomic projects. Surprisingly, the development of electrophoretic methods in the last 3 years looks like a “passed-on topic”. In ten years we moved from identifying at most 500 species in complex samples to identifying 60% of the human proteome.

The problem of PTMs was also addressed in the paper, which labeled it as a significant concern for biologist due to the fundamental role PTMs play in the regulation of cellular behavior. Today, new and better MS protocols and workflows for studying PTMs continue to be developed, as the existing alternatives do not yet provide a definitive solution to this problem.
But one of the best contributions of Mann & Aebersold in this manuscript was to discuss, for the benefit of the proteomics community, the problems of analysis, visualization and storage of MS data and results. Early on, Aebersold created the TransProteomic Pipeline Project, the PeptideAtlas and a complete set of tools and algorithms to analyze proteomics data. Also, he trained vast number of PI’s and PostDoc’s in the field of computational proteomics around the world. He is a founder in the field of spectral library algorithms, quality assignment of protein identifications and data storage. Mann recently created the popular and well-known platform MaxQuant for Proteomics Studies using High-Quality spectra.

“The analysis and interpretation of the enormous volumes of proteomic data remains an unsolved challenge, particularly for gel-free approaches. Expert manual analysis is incompatible with the tens of thousands of spectra collected in a single experiment and is inconsistent. Therefore, the development of transparent tools for the analysis of proteomic data using statistical principles is a key challenge. Only once such tools are tested, validated and widely accepted will it become feasible to apply quality standards for protein identification, quantification and other measurements and to compare complementary proteomic data sets generated in different laboratories. These comparisons will also depend critically on transparent file structures for data storage, communication and visualization. The development of such proteomics tools is still in its
Aebersold & Matthias Mann 2003

Together, Mann and Aebersold foreboded the dramatic growth and development that MS-based proteomics has enjoyed together with Computational Proteomics. From my point of view and it was also included in the manuscript “Computational Proteomics Pitfalls and Challenges: HavanaBioinfo 2012 Workshop Report”; in the near future “Experimentalists (Biologist or Spectrometrist) need to realize that they are doomed without bioinformatics and statistical knowledge in current science”. The abundance of information presents many hurdles to the investigators who need to interpret proteomics data and derive new biological insights. Therefore, efforts need to focus on two directions: (i) computational proteomics software needs to become more intuitive; (ii) bioinformatics and statistics knowledge is mandatory to understand the overall behavior of biological results. New bioinformatics applications need to be more professional in terms of error-tolerance, usability, and data integration; and researchers in life sciences need to take bioinformatics and statistics courses.           

Thanks to Mann & Aebersold and happy anniversary to their manuscript!!! 

Wiśniewski JR, Zougman A, Nagaraj N, Mann M, Universal sample preparation method for proteome analysis. Nat Methods. 2009 May;6(5):359-62. doi: 10.1038/nmeth.1322. Epub 2009 Apr 19. PMID: 19377485

Heller M, Ye M, Michel PE, Morier P, Stalder D, Jünger MA, Aebersold R, Reymond F, Rossier JS. Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides. J Proteome Res. 2005 Nov-Dec;4(6):2273-82. PMID: 16335976