Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

Meier, Florian; Brunner, Andreas David; Koch, Scarlet; Koch, Heiner; Lubeck, Markus; Krause, Michael; Goedecke, Niels; Decker, Jens; Kosinski, Thomas; Park, Melvin A.; Bache, Nicolai; Hoerning, Ole; Cox, Jürgen; Räther, Oliver; Mann, Matthias

doi:10.1074/mcp.tir118.000900

Cited by 760 publications

(715 citation statements)

References 53 publications

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“…Ion mobility spectrometry (1-3) (IMS) separates molecules in the gas phase by their collisional cross section (CCS) which is the effective area of a molecule quantifying the likelihood of scattering events with the gas. It can be coupled to mass spectrometry (MS) for which it constitutes a separation dimension in addition to mass over charge (m/z).Together with liquid chromatography (LC) and tandem mass spectrometry (MS/MS) one obtains LC-IMS-MS/MS shotgun proteomics, a promising strategy for the analysis of complex samples (4)(5)(6)(7).Specifically, the object of our studies is the timsTOF Pro instrument (8) which is a time-of-flight (TOF) mass spectrometer utilizing a trapped ion mobility spectrometry (9-11) (TIMS)device operated with the parallel accumulationserial fragmentation (PASEF) scan mode (12).…”

Section: Introductionmentioning

confidence: 99%

MaxQuant software for ion mobility enhanced shotgun proteomics

Prianichnikov

Koch

et al. 2019

Preprint

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Ion mobility can add a dimension to LC-MS based shotgun proteomics which has the potential to boost proteome coverage, quantification accuracy and dynamic range. Required for this is suitable software that extracts the information contained in the fourdimensional (4D) data space spanned by m/z, retention time, ion mobility and signal intensity. Here we describe the ion mobility enhanced MaxQuant software, which utilizes the added data dimension. It offers an end to end computational workflow for the identification and quantification of peptides, proteins and posttranslational modification sites in LC-IMS-MS/MS shotgun proteomics data. We apply it to trapped ion mobility spectrometry (TIMS) coupled to a quadrupole time-of-flight (QTOF) analyzer. A highly parallelizable 4D feature detection algorithm extracts peaks which are assembled to isotope patterns. Masses are recalibrated with a non-linear m/z, retention time, ion mobility and signal intensity dependent model, based on peptides from the sample. A new matching between runs (MBR) algorithm that utilizes collisional cross section (CCS) values of MS1 features in the matching process significantly gains specificity from the extra dimension. Prerequisite for using CCS values in MBR is a relative alignment of the ion mobility values between the runs. The missing value problem in protein quantification over many samples is greatly reduced by CCS aware MBR.MS1 level label-free quantification is also implemented which proves to be highly precise and accurate on a benchmark dataset with known ground truth. MaxQuant for LC-IMS-MS/MS is part of the basic MaxQuant release and can be downloaded from http://maxquant.org. 3

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Section: Introductionmentioning

confidence: 99%

MaxQuant software for ion mobility enhanced shotgun proteomics

Prianichnikov

Koch

et al. 2019

Preprint

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“…With the constant emergence of novel biomarker‐related proteolytic events, the readily generated datasets could also be easily re‐examined and validated without the need for additional sample analysis. Another new technology that can trace its roots to ion mobility is PASEF (parallel sensitivity–serial fragmentation), which scans hundreds of MS/MS events per second at full sensitivity, thereby making it possible to detect even reporters of extremely low abundance . Technologies like SWATH and PASEF are still relatively new and, despite their numerous analytical benefits, it will take some time for them to become fully integrated into degradomic research.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Degradomics in Biomarker Discovery

Grozdanić

Vidmar

Vizovišek

et al. 2019

Proteomics Clinical Apps

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The upregulation of protease expression and proteolytic activity is implicated in numerous pathological conditions such as neurodegeneration, cancer, cardiovascular and autoimmune diseases, and bone degeneration. During disease progression, various proteases form characteristic patterns of cleaved proteins and peptides, which can affect disease severity and course of progression. It has been shown that qualitative and quantitative monitoring of cleaved protease substrates can provide relevant prognostic, diagnostic, and therapeutic information. As proteolytic fragments and peptides generated in the affected tissue are commonly translocated to blood, urine, and other proximal fluids, their possible application as biomarkers is the subject of ongoing research. The field of degradomics has been established to enable the global identification of proteolytic events on the organism level, utilizing proteomic approaches and sample preparation techniques that facilitate the detection of proteolytic processing of protease substrates in complex biological samples. In this review, some of the latest developments in degradomic methodologies used for the identification and validation of biologically relevant proteolytic events and their application in the search for clinically relevant biomarker candidates are presented. The current state of degradomics in clinics is discussed and the future perspectives of the field are outlined.

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“…In a TIMSquadrupole-TOF configuration, the release of precursor ions can be synchronized with the quadrupole selection in a method termed parallel accumulation followed by serial fragmentation 19 . PASEF achieves a more than ten-fold increase in sequencing speed in data dependent acquisition, without the loss of sensitivity that is otherwise inherent to very fast fragmentation cycles 20,21 .…”

Section: Introductionmentioning

confidence: 99%

Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage

Meier

Brunner

Frank

et al. 2019

Preprint

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Data independent acquisition (DIA) modes isolate and concurrently fragment populations of different precursors by cycling through segments of a predefined precursor m/z range. Although these selection windows collectively cover the entire m/z range, overall only a few percent of all incoming ions are sampled. Making use of the correlation of molecular weight and ion mobility in a trapped ion mobility device (timsTOF Pro), we here devise a novel scan mode that samples up to 100% of the peptide precursor ion current. We extend an established targeted data extraction workflow by including the ion mobility dimension for both signal extraction and scoring, thereby increasing the specificity for precursor identification. Data acquired from whole proteome digests and mixed organism samples demonstrate deep proteome coverage and a very high degree of reproducibility as well as quantitative accuracy, even from 10 ng sample amounts.

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Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

Cited by 760 publications

References 53 publications

MaxQuant software for ion mobility enhanced shotgun proteomics

MaxQuant software for ion mobility enhanced shotgun proteomics

Degradomics in Biomarker Discovery

Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage

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