Multi-Reference Spectral Library Yields Almost Complete Coverage of Heterogeneous LC-MS/MS Data Sets

Journal of Proteome Research
Constantin AmmarRalf Zimmer

Abstract

Spectral libraries play a central role in the analysis of data-independent-acquisition (DIA) proteomics experiments. A main assumption in current spectral library tools is that a single characteristic intensity pattern (CIP) suffices to describe the fragmentation of a peptide in a particular charge state (peptide charge pair). However, we find that this is often not the case. We carry out a systematic evaluation of spectral variability over public repositories and in-house data sets. We show that spectral variability is widespread and partly occurs under fixed experimental conditions. Using clustering of preprocessed spectra, we derive a limited number of multiple characteristic intensity patterns (MCIPs) for each peptide charge pair, which allow almost complete coverage of our heterogeneous data set without affecting the false discovery rate. We show that a MCIP library derived from public repositories performs in most cases similar to a "custom-made" spectral library, which has been acquired under identical experimental conditions as the query spectra. We apply the MCIP approach to a DIA data set and observe a significant increase in peptide recognition. We propose the MCIP approach as an easy-to-implement addition to current...Continue Reading

References

Jan 5, 2002·Journal of the American Society for Mass Spectrometry·Katty X WanMichael L Gross
Mar 14, 2003·Nature·Ruedi Aebersold, Matthias Mann
Feb 21, 2004·Bioinformatics·Robertson Craig, Ronald C Beavis
Dec 31, 2005·Nucleic Acids Research·Frank DesiereRuedi Aebersold
Dec 31, 2005·Nucleic Acids Research·Philip JonesRolf Apweiler
Apr 15, 2006·Science·Bruno Domon, Ruedi Aebersold
Jun 7, 2006·Rapid Communications in Mass Spectrometry : RCM·Robert S PlumbJeremy K Nicholson
Aug 8, 2006·Journal of Proteome Research·R CraigR C Beavis
Aug 16, 2006·Analytical Chemistry·Barbara E FrewenMichael J MacCoss
May 31, 2008·Molecular & Cellular Proteomics : MCP·Alexander SchmidtBruno Domon
Sep 23, 2008·Nature Methods·Henry LamRuedi Aebersold
Jul 4, 2009·Analytical Chemistry·Alexandre PanchaudDavid R Goodlett
Jul 17, 2009·Journal of Proteome Research·Carly A SherwoodDaniel B Martin
Oct 2, 2009·Proteomics·Michael Riffle, Jimmy K Eng
Jan 29, 2010·Bioinformatics·Paulo C CarvalhoJohn R Yates
Mar 30, 2010·Molecular & Cellular Proteomics : MCP·Jian WangNuno Bandeira
Jul 9, 2010·Molecular & Cellular Proteomics : MCP·Tamar GeigerMatthias Mann
Jan 25, 2011·Journal of Proteome Research·Jürgen CoxMatthias Mann
Feb 24, 2011·Analytical Chemistry·Alexandre PanchaudDavid R Goodlett
May 3, 2011·Molecular & Cellular Proteomics : MCP·Chia-Yu YenWilliam M Old
Oct 12, 2012·Nature Biotechnology·Matthew C ChambersParag Mallick
Nov 20, 2012·Journal of Proteomics·Sebastien GallienBruno Domon
Dec 4, 2012·Nucleic Acids Research·Juan Antonio VizcaínoHenning Hermjakob
Sep 1, 1994·Journal of the American Society for Mass Spectrometry·S E Stein, D R Scott
Nov 1, 1994·Journal of the American Society for Mass Spectrometry·J K EngJ R Yates
Apr 15, 2014·Nature Biotechnology·Hannes L RöstRuedi Aebersold
Jan 20, 2015·Nature Methods·Chih-Chiang TsouAlexey I Nesvizhskii
Feb 13, 2015·Nature Protocols·Olga T SchubertRuedi Aebersold
Jan 1, 2014·Scientific Data·George RosenbergerRuedi Aebersold
Dec 1, 2015·Proteomics·Johannes Griss
May 11, 2016·Molecular & Cellular Proteomics : MCP·Jemma X WuMark P Molloy
Nov 1, 2016·Nature Biotechnology·Pedro NavarroStefan Tenzer
Jan 31, 2017·Nature Methods·Daniel P ZolgBernhard Kuster

❮ Previous
Next ❯

Citations

Dec 28, 2019·Analytical Chemistry·Carolina Fernández-CostaJohn R Yates
Dec 18, 2020·Journal of Proteome Research·Guo Ci TeoAlexey I Nesvizhskii

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.