False discovery rate: the Achilles' heel of proteogenomics
Proteogenomics refers to the integrated analysis of the genome and proteome that
leverages mass-spectrometry (MS)-based proteomics data to improve genome annotations …
leverages mass-spectrometry (MS)-based proteomics data to improve genome annotations …
Limitations and pitfalls in protein identification by mass spectrometry
G Lubec, L Afjehi-Sadat - Chemical reviews, 2007 - ACS Publications
The advent of proteomics techniques for protein identification (PrI) represented a major step
forward in protein chemistry, 1, 2 and indeed, a legion of laboratories are now using different …
forward in protein chemistry, 1, 2 and indeed, a legion of laboratories are now using different …
The plant cell wall–decomposing machinery underlies the functional diversity of forest fungi
DC Eastwood, D Floudas, M Binder, A Majcherczyk… - Science, 2011 - science.org
Brown rot decay removes cellulose and hemicellulose from wood—residual lignin
contributing up to 30% of forest soil carbon—and is derived from an ancestral white rot …
contributing up to 30% of forest soil carbon—and is derived from an ancestral white rot …
PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation
The role of PPM1D mutations in de novo gliomagenesis has not been systematically
explored. Here we analyze whole genome sequences of 170 pediatric high-grade gliomas …
explored. Here we analyze whole genome sequences of 170 pediatric high-grade gliomas …
Deep proteomics identifies shared molecular pathway alterations in synapses of patients with schizophrenia and bipolar disorder and mouse model
Synaptic dysfunction is implicated in the pathophysiology of schizophrenia (SCZ) and
bipolar disorder (BP). We use quantitative mass spectrometry to carry out deep, unbiased …
bipolar disorder (BP). We use quantitative mass spectrometry to carry out deep, unbiased …
Mass spectrometric detection of marker peptides in tryptic digests of gelatin: a new method to differentiate between bovine and porcine gelatin
G Zhang, T Liu, Q Wang, L Chen, J Lei, J Luo, G Ma… - Food …, 2009 - Elsevier
Gelatin is a mixture of polypeptides obtained by hydrolysis of collagen primarily from bovine
and porcine skin and bones. The similarity between different gelatins makes it difficult to …
and porcine skin and bones. The similarity between different gelatins makes it difficult to …
A novel method to differentiate bovine and porcine gelatins in food products: NanoUPLC-ESI-Q-TOF-MSE based data independent acquisition technique to detect …
We presented a novel nanoUPLC-MS E workflow method that has potential to identify origin
of gelatin in some dairy products; yoghurt, cheese and ice cream. In this study, the method …
of gelatin in some dairy products; yoghurt, cheese and ice cream. In this study, the method …
MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions
Multiple reaction monitoring (MRM) of peptides uses tandem mass spectrometry to quantify
selected proteins of interest, such as those previously identified in differential studies. Using …
selected proteins of interest, such as those previously identified in differential studies. Using …
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
LC‐MS experiments can generate large quantities of data, for which a variety of database
search engines are available to make peptide and protein identifications. Decoy databases …
search engines are available to make peptide and protein identifications. Decoy databases …
Quantitative proteomic approach to study subcellular localization of membrane proteins
PG Sadowski, TPJ Dunkley, IP Shadforth, P Dupree… - Nature protocols, 2006 - nature.com
As proteins within cells are spatially organized according to their role, knowledge about
protein localization gives insight into protein function. Here, we describe the LOPIT …
protein localization gives insight into protein function. Here, we describe the LOPIT …