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      Inferring Protein-Protein Interaction Networks From Mass Spectrometry-Based Proteomic Approaches: A Mini-Review

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          Abstract

          Studying protein-protein interaction networks provide key evidence for the underlying molecular mechanisms. Mass spectrometry-based proteomic approaches have been playing a pivotal role in deciphering these interaction networks, along with precise quantification for individual interactions. In this mini-review we discuss the available techniques and methods for qualitative and quantitative elucidation of protein-protein interaction networks. We then summarize the down-stream computational strategies for identification and quantification of interactions from those techniques. Finally, we highlight the challenges and limitations of current computational pipelines in eliminating false positive interactors, followed by a summary of the innovative algorithms to address these issues, along with the scope for future improvements.

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          Most cited references 106

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          A statistical model for identifying proteins by tandem mass spectrometry.

          A statistical model is presented for computing probabilities that proteins are present in a sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a proteolytic digest of the sample. Peptides that correspond to more than a single protein in the sequence database are apportioned among all corresponding proteins, and a minimal protein list sufficient to account for the observed peptide assignments is derived using the expectation-maximization algorithm. Using peptide assignments to spectra generated from a sample of 18 purified proteins, as well as complex H. influenzae and Halobacterium samples, the model is shown to produce probabilities that are accurate and have high power to discriminate correct from incorrect protein identifications. This method allows filtering of large-scale proteomics data sets with predictable sensitivity and false positive identification error rates. Fast, consistent, and transparent, it provides a standard for publishing large-scale protein identification data sets in the literature and for comparing the results obtained from different experiments.
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            Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ *

            Protein quantification without isotopic labels has been a long-standing interest in the proteomics field. However, accurate and robust proteome-wide quantification with label-free approaches remains a challenge. We developed a new intensity determination and normalization procedure called MaxLFQ that is fully compatible with any peptide or protein separation prior to LC-MS analysis. Protein abundance profiles are assembled using the maximum possible information from MS signals, given that the presence of quantifiable peptides varies from sample to sample. For a benchmark dataset with two proteomes mixed at known ratios, we accurately detected the mixing ratio over the entire protein expression range, with greater precision for abundant proteins. The significance of individual label-free quantifications was obtained via a t test approach. For a second benchmark dataset, we accurately quantify fold changes over several orders of magnitude, a task that is challenging with label-based methods. MaxLFQ is a generic label-free quantification technology that is readily applicable to many biological questions; it is compatible with standard statistical analysis workflows, and it has been validated in many and diverse biological projects. Our algorithms can handle very large experiments of 500+ samples in a manageable computing time. It is implemented in the freely available MaxQuant computational proteomics platform and works completely seamlessly at the click of a button.
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              Mass spectrometry-based proteomics.

              Recent successes illustrate the role of mass spectrometry-based proteomics as an indispensable tool for molecular and cellular biology and for the emerging field of systems biology. These include the study of protein-protein interactions via affinity-based isolations on a small and proteome-wide scale, the mapping of numerous organelles, the concurrent description of the malaria parasite genome and proteome, and the generation of quantitative protein profiles from diverse species. 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.
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                Author and article information

                Contributors
                Journal
                Comput Struct Biotechnol J
                Comput Struct Biotechnol J
                Computational and Structural Biotechnology Journal
                Research Network of Computational and Structural Biotechnology
                2001-0370
                20 June 2019
                2019
                20 June 2019
                : 17
                : 805-811
                Affiliations
                [a ]Department of Computational Biology, Cornell University, Ithaca, New York 14853, USA
                [b ]Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
                Author notes
                [* ]Corresponding author at: Department of Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA haiyuan.yu@ 123456cornell.edu
                [1]

                The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

                Article
                S2001-0370(19)30091-1
                10.1016/j.csbj.2019.05.007
                6611912
                © 2019 The Authors

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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