Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammalian cells, because reduced protein levels reduce the number of confidently sequenced peptides. To alleviate this reduction, we developed Data-driven Alignment of Retention Times for IDentification (DART-ID). DART-ID implements principled Bayesian frameworks for global retention time (RT) alignment and for incorporating RT estimates towards improved confidence estimates of peptide-spectrum-matches. When applied to bulk or to single-cell samples, DART-ID increased the number of data points by 30-50% at 1% FDR, and thus decreased missing data. Benchmarks indicate excellent quantification of peptides upgraded by DART-ID and support their utility for quantitative analysis, such as identifying cell types and cell-type specific proteins. The additional datapoints provided by DART-ID boost the statistical power and double the number of proteins identified as differentially abundant in monocytes and T-cells. DART-ID can be applied to diverse experimental designs and is freely available at http://dart-id.slavovlab.net.

Transcriptional and post-transcriptional regulation shape tissue-type-specific proteomes, but their relative contributions remain contested. Estimates of the factors determining protein levels in human tissues do not distinguish between (i) the factors determining the variability between the abundances of different proteins, i.e., mean-level-variability and, (ii) the factors determining the physiological variability of the same protein across different tissue types, i.e., across-tissues variability. We sought to estimate the contribution of transcript levels to these two orthogonal sources of variability, and found that scaled mRNA levels can account for most of the mean-level-variability but not necessarily for across-tissues variability. The reliable quantification of the latter estimate is limited by substantial measurement noise. However, protein-to-mRNA ratios exhibit substantial across-tissues variability that is functionally concerted and reproducible across different datasets, suggesting extensive post-transcriptional regulation. These results caution against estimating protein fold-changes from mRNA fold-changes between different cell-types, and highlight the contribution of post-transcriptional regulation to shaping tissue-type-specific proteomes.

We study the total least squares (TLS) problem that generalizes least squares regression by allowing measurement errors in both dependent and independent variables. TLS is widely used in applied fields including computer vision, system identification and econometrics. The special case when all dependent and independent variables have the same level of uncorrelated Gaussian noise, known as ordinary TLS, can be solved by singular value decomposition (SVD). However, SVD cannot solve many important practical TLS problems with realistic noise structure, such as having varying measurement noise, known structure on the errors, or large outliers requiring robust error-norms. To solve such problems, we develop convex relaxation approaches for a general class of structured TLS (STLS). We show both theoretically and experimentally, that while the plain nuclear norm relaxation incurs large approximation errors for STLS, the re-weighted nuclear norm approach is very effective, and achieves better accuracy on challenging STLS problems than popular non-convex solvers. We describe a fast solution based on augmented Lagrangian formulation, and apply our approach to an important class of biological problems that use population average measurements to infer cell-type and physiological-state specific expression levels that are very hard to measure directly.

The attempt to elucidate biological pathways and classify genes has led to the development of numerous clustering approaches to gene expression. All these approaches use a single metric to identify genes with similar expression levels. Until now, the correlation between the expression levels of such genes has been based on phenomenological and heuristic correlation functions, rather than on biological models. In this paper, we derive six distinct correlation functions based on explicit thermodynamic modeling of gene regulatory networks. We then combine these correlation functions with novel biclustering algorithms to identify functionally enriched groups. The statistical significance of the identified groups is demonstrated by precision-recall curves and calculated p-values. Furthermore, comparison with chromatin immunoprecipitation data indicates that the performance of the derived correlation functions depends on the specific regulatory mechanisms. Finally, we introduce the idea of multi-class biclustering and with the help of support vector machines we demonstrate its improved classification performance in a microarray dataset.