Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF

Data-independent acquisition (DIA) methods have become increasingly attractive in mass spectrometry–based proteomics because they enable high data completeness and a wide dynamic range. Recently, we combined DIA with parallel accumulation–serial fragmentation (dia-PASEF) on a Bruker trapped ion mobility (IM) separated quadrupole time-of-flight mass spectrometer. This requires alignment of the IM separation with the downstream mass selective quadrupole, leading to a more complex scheme for dia-PASEF window placement compared with DIA. To achieve high data completeness and deep proteome coverage, here we employ variable isolation windows that are placed optimally depending on precursor density in the m/z and IM plane. This is implemented in the freely available py_diAID (Python package for DIA with an automated isolation design) package. In combination with in-depth project-specific proteomics libraries and the Evosep liquid chromatography system, we reproducibly identified over 7700 proteins in a human cancer cell line in 44 min with quadruplicate single-shot injections at high sensitivity. Even at a throughput of 100 samples per day (11 min liquid chromatography gradients), we consistently quantified more than 6000 proteins in mammalian cell lysates by injecting four replicates. We found that optimal dia-PASEF window placement facilitates in-depth phosphoproteomics with very high sensitivity, quantifying more than 35,000 phosphosites in a human cancer cell line stimulated with an epidermal growth factor in triplicate 21 min runs. This covers a substantial part of the regulated phosphoproteome with high sensitivity, opening up for extensive systems-biological studies.

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Optimal dia-PASEF window design with py_diAID combined with deep libraries.

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Quantification of the HeLa cell proteome to a depth of >7700 in only 44 min.

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Ion mobility–resolved phosphoproteomics determines >35,000 class I phosphosites.

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py_diAID is freely available as GUI, CLI, and Python modules.

Chirality of aromatic bis-imides from their circular dichroism spectra

It is demonstrated that chirality of molecules composed of 1,2,4, 5-benzenetetracarboxydiimide (pyromellitic diimide) or 1,4,5, 8-naphthalenetetracarboxydiimide units is reflected by their exciton Cotton effects. The analysis is based on the calculated (ZINDO/S) excited states of the model diimide chromophores 1a and 2a. Rotation of the diimide chromophores around the C-N bond in diimides 3-5 is evaluated from the dynamic (1)H NMR data. A comparison of chiroptical properties of bis-diimides 3-5 with the CD spectra of bis-imides 6-8 is also presented. Copyright 2000 Wiley-Liss, Inc.

Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome

Single-cell proteomics by mass spectrometry is emerging as a powerful and unbiased method for the characterization of biological heterogeneity. So far, it has been limited to cultured cells, whereas an expansion of the method to complex tissues would greatly enhance biological insights. Here we describe single-cell Deep Visual Proteomics (scDVP), a technology that integrates high-content imaging, laser microdissection and multiplexed mass spectrometry. scDVP resolves the context-dependent, spatial proteome of murine hepatocytes at a current depth of 1,700 proteins from a cell slice. Half of the proteome was differentially regulated in a spatial manner, with protein levels changing dramatically in proximity to the central vein. We applied machine learning to proteome classes and images, which subsequently inferred the spatial proteome from imaging data alone. scDVP is applicable to healthy and diseased tissues and complements other spatial proteomics and spatial omics technologies.

A fluorescence-microscopic and flow-cytometric study of HeLa cells with an experimentally induced respiratory deficiency

HeLa cells, cultured over a long period in a medium containing low doses of ethidiumbromide, were used as a model system for flow-cytometric detection of human cells with impaired mitochondrial respiratory function. Based on laserscan and flowcytometric analysis after rhodamine 123 staining, the mitochondrial membrane potential of respiratory deficient cells seems unchanged as compared to control cells. Maintenance of this membrane potential in respiration-impaired cells requires glycolytic ATP generation, as transient inhibition of glycolysis by sodium fluoride affects rhodamine 123 accumulation in ethidiumbromide-treated cells, but not in control cells. We present a protocol which allows the detection and separation of respiratory deficient cells by flow cytometry.

Atomic-resolution chemical characterization of (2x)72-kDa tryptophan synthase via four- and five-dimensional 1H-detected solid-state NMR

NMR chemical shifts provide detailed information on the chemical properties of molecules, thereby complementing structural data from techniques like X-ray crystallography and electron microscopy. Detailed analysis of protein NMR data, however, often hinges on comprehensive, site-specific assignment of backbone resonances, which becomes a bottleneck for molecular weights beyond 40 to 45 kDa. Here, we show that assignments for the (2x)72-kDa protein tryptophan synthase (665 amino acids per asymmetric unit) can be achieved via higher-dimensional, proton-detected, solid-state NMR using a single, 1-mg, uniformly labeled, microcrystalline sample. This framework grants access to atom-specific characterization of chemical properties and relaxation for the backbone and side chains, including those residues important for the catalytic turnover. Combined with first-principles calculations, the chemical shifts in the β-subunit active site suggest a connection between active-site chemistry, the electrostatic environment, and catalytically important dynamics of the portal to the β-subunit from solution.

Flow cytometry as a tool to discriminate respiratory-competent and respiratory-deficient yeast cells

The cationic lipophilic dye Rhodamine 123 (Rh123) is selectively enriched in mitochondria in a membrane potential-dependent manner. Application of drugs which interfere with the electron flow of the respiratory chain lead to a severe reduction of mitochondrial dye uptake. In this communication we show that the same effect is observed after Rh123-staining of respiratory-deficient yeast mutants. Based on this observation we used flow cytometry to discriminate respiratory-competent and respiratory-deficient yeast cells. Combined with a cell sorter we were able to selectively enrich respiring and non-respiring yeast cells, respectively, from a mixture of cells.

1,8-Naphthalimides as Stereochemical Probes for Chiral Amines: A Study of Electronic Transitions and Exciton Coupling

The absorption and magnetic circular dichroism (MCD) spectra of 1,8-naphthalimide are analyzed in terms of the number of contributing electronic transitions and their polarization. The experimental results are supported by semiempirical INDO/S calculations. It is demonstrated that the strongly allowed, pi --> pi naphthalene transition of the 1,8-naphthalimide chromophore located at 231 nm is perfectly suited for absolute configuration assignments of amine derivatives on the basis of the bichromophoric exciton coupling. Both degenerate (bis-1,8-naphthalimide) and nondegenerate (1,8-naphthalimide-phthalimide, 1,8-naphthalimide-phenyl, or 1,8-naphthalimide-benzoate) couplings were studied. In the latter case, the sign of the exciton Cotton effect was opposite to the sign of the degenerate exciton Cotton effect for the same absolute configuration. An extension of the application of the exciton coupling to the 264 nm pi --> pi transition of 1,9-anthraimide is also shown.

Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel

Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput, and robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mDIA). We demonstrate automated and complete dimethyl labeling of bulk or single-cell samples, without losing proteomic depth. Lys-N digestion enables five-plex quantification at MS1 and MS2 level. Because the multiplexed channels are quantitatively isolated from each other, mDIA accommodates a reference channel that does not interfere with the target channels. Our algorithm RefQuant takes advantage of this and confidently quantifies twice as many proteins per single cell compared to our previous work (Brunner et al, PMID 35226415), while our workflow currently allows routine analysis of 80 single cells per day. Finally, we combined mDIA with spatial proteomics to increase the throughput of Deep Visual Proteomics seven-fold for microdissection and four-fold for MS analysis. Applying this to primary cutaneous melanoma, we discovered proteomic signatures of cells within distinct tumor microenvironments, showcasing its potential for precision oncology.

Synchro-PASEF Allows Precursor-Specific Fragment Ion Extraction and Interference Removal in Data-Independent Acquisition

Data-independent acquisition (DIA) methods have become increasingly popular in mass spectrometry-based proteomics because they enable continuous acquisition of fragment spectra for all precursors simultaneously. However, these advantages come with the challenge of correctly reconstructing the precursor-fragment relationships in these highly convoluted spectra for reliable identification and quantification. Here, we introduce a scan mode for the combination of trapped ion mobility spectrometry with parallel accumulation-serial fragmentation (PASEF) that seamlessly and continuously follows the natural shape of the ion cloud in ion mobility and peptide precursor mass dimensions. Termed synchro-PASEF, it increases the detected fragment ion current several-fold at sub-second cycle times. Consecutive quadrupole selection windows move synchronously through the mass and ion mobility range. In this process, the quadrupole slices through the peptide precursors, which separates fragment ion signals of each precursor into adjacent synchro-PASEF scans. This precisely defines precursor-fragment relationships in ion mobility and mass dimensions and effectively deconvolutes the DIA fragment space. Importantly, the partitioned parts of the fragment ion transitions provide a further dimension of specificity via a lock-and-key mechanism. This is also advantageous for quantification, where signals from interfering precursors in the DIA selection window do not affect all partitions of the fragment ion, allowing to retain only the specific parts for quantification. Overall, we establish the defining features of synchro-PASEF and explore its potential for proteomic analyses.

AlphaTims: Indexing Trapped Ion Mobility Spectrometry-TOF Data for Fast and Easy Accession and Visualization

High-resolution MS-based proteomics generates large amounts of data, even in the standard LC-tandem MS configuration. Adding an ion mobility dimension vastly increases the acquired data volume, challenging both analytical processing pipelines and especially data exploration by scientists. This has necessitated data aggregation, effectively discarding much of the information present in these rich datasets. Taking trapped ion mobility spectrometry (TIMS) on a quadrupole TOF (Q-TOF) platform as an example, we developed an efficient indexing scheme that represents all data points as detector arrival times on scales of minutes (LC), milliseconds (TIMS), and microseconds (TOF). In our open-source AlphaTims package, data are indexed, accessed, and visualized by a combination of tools of the scientific Python ecosystem. We interpret unprocessed data as a sparse four-dimensional matrix and use just-in-time compilation to machine code with Numba, accelerating our computational procedures by several orders of magnitude while keeping to familiar indexing and slicing notations. For samples with more than six billion detector events, a modern laptop can load and index raw data in about a minute. Loading is even faster when AlphaTims has already saved indexed data in an HDF5 file, a portable scientific standard used in extremely large-scale data acquisition. Subsequently, data accession along any dimension and interactive visualization happens in milliseconds. We have found AlphaTims to be a key enabling tool to explore high-dimensional LC-TIMS-Q-TOF data and have made it freely available as an open-source Python package with a stand-alone graphical user interface at https://github.com/MannLabs/alphatims or as part of the AlphaPept 'ecosystem'.

High-Throughput Mass Spectrometry-Based Proteomics with dia-PASEF

Ion mobility separation is becoming an integral part in mass spectrometry-based proteomics. Here we describe the use of a trapped ion mobility-quadrupole time-of-flight (TIMS-QTOF) mass spectrometer for high-throughput label-free quantification with data-independent acquisition. The parallel accumulation-serial fragmentation (PASEF) operation mode positions the mass-selecting quadrupole as a function of the TIMS separation, which allows highly efficient data-independent acquisition schemes (dia-PASEF), but also increases complexity in the method design. We provide a step-by-step protocol for instrument setup, method design, data acquisition and ion mobility-aware, library-based data analysis with Spectronaut. We highlight key acquisition parameters and illustrate their optimization for short gradients. Using the EvosepOne liquid chromatography system, we demonstrate expected results for the analysis of a human cancer cell line at a throughput of 60 samples per day, leading to the quantification of about 6000 protein groups with very high reproducibility. Importantly, the protocol can be readily adapted to other gradients and sample types such as modified peptides.

Prediction of nutritional status and intestinal tumor involvement in patients with primary or recurrent ovarian cancer: Results of a prospective study

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Background: Global malnutrition is widespread among patients with ovarian cancer. The objective of this study was to investigate the influence of the nutritional status on the clinical outcome of patients with primary or recurrent ovarian and peritoneal cancer. Methods: In a two-year-period (January 2007 - December 2008) 152 consecutive patients were analysed. 79 (52%) of them had primary and 73 (48%) recurrent disease. At the time of admission for surgical therapy, the body composition was analysed with Bioelectrical Impedance Analysis (BIA) using phase angle alpha and ratio of extra-cellular mass and body cell mass (ECM/BCM). Serum protein parameters were registered. The risk of malnutrition was estimated by Nutritional Risk Score (NRS). During operation a standardised and validated tumor documentation tool (IMO) was performed. Nutritional parameters were correlated with IMO-parameters. Results: The median age of patients was 56 years (range 48–66) with median BMI 24.4 kg/m2 (range 21.8–27.3). In 23% primary and 14% recurrent cases a high nutritional risk was classified (NRS≥3). These patients had significantly lower serum albumin, pre-albumin and transferrin levels compared to patients with NRS<3 (p < 0.05). FIGO stage and NRS correlated negatively with phase angle alpha and positively with ECM/BCM in patients with primary diagnosis (p < 0.05). Patients with primary or recurrent disease who required surgical resection of small or large intestine, phase angle alpha and serum albumin level were significantly lower than in patients with no intestinal involvement (p < 0.05). Conclusions: Independent of tumor stage, the preoperative evaluation of BIA, especially phase angle α, is a valid method to predict surgical outcome in patients with ovarian and peritoneal cancer.

No significant financial relationships to disclose.

Disseminated neocortical and subcortical encephalopathy (DNSE) with widespread activation of brain macrophages: a new dementia disorder? Autopsy reports of two postmenopausal women from families with mitochondrial DNA mutations

In this study we present 2 postmenopausal women who showed clinical symptoms that resembled those of a rather well-defined group of vascular dementia disorders, termed subcortical dementia (Binswanger disease, CADASIL). Patient 1 exhibited mitochondrial DNA (mtDNA) variants in the ND5 gene at position 13,708 and the Cytb gene at position 15,257. These DNA variants have been described in a number of neurologic disorders, but their pathogenetic potential is unclear. Patient 2 showed the same DNA alterations and an additional mtDNA variant at position 15,812 in the Cytb gene. The principal neurohistologic features of the 2 atrophic brains presented here include: subtotal selective neuronal cell loss in the cortex and, to a lesser degree, in the basal ganglia (claustrum, putamen, globus pallidus), sparing palaeocortex and periarchaeocortex, and a very characteristic and diagnostic feature was detachment of astrocytic processes from capillary walls resulting in pericapillary space formation. These pericapillary spaces were partially filled with macrophages. The spaces were not associated with total breakdown of the blood vessel walls as demonstrated by the absence of erythrocytes, lymphocytes, or polymorphonuclear leukocytes outside the vascular bed of the brain; progressive subcortical encephalopathy, as it is seen in subcortical dementia (Binswanger), but lacking arterial lipohyalinosis. The cerebral grey and white matter revealed cuffing of arteries and arterioles by adventitial macrophages. The neocortical and subcortical changes were accompanied by myriads of activated macrophages filled with lipids. The pathology of our 2 cases differs from that of other neurodegenerative disorders and we suggest the term of "disseminated neocortical and subcortical encephalopathy (DNSE) with widespread activation of brain macrophages".

Impact of malnutrition on surgical outcome of patients with ovarian cancer: Results of a prospective study

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Background: The purpose of this study was to examine an influence of poor nutritional status on surgical outcome in patients with ovarian cancer. Methods: Data from 152 consecutive patients with histologically confirmed ovarian cancer were prospectively analyzed. Overall 79 suffered from primary and 73 from recurrent disease. All patients received a systematic nutritional assessment prior to cytoreductive surgery and postoperative all complications were analyzed in detail. The Nutritional Risk Score (NRS-2002) was used to identify patients at high nutritional risk (NRS≥3). Intraoperatively, a standardized documentation script (IMO) was applied including tumor localization, surgical interventions, and postoperative residual tumor mass. Results: 29 patients (19%) were classified as malnourished, including 19 (24%) with primary and 10 (14%) with recurrent disease. These patients showed a significantly poorer performance status preoperatively compared to patients with NRS<3 (p < 0.05), which was assessed according to the American Society of Anesthesiologists (ASA). Also an intra-operatively documented tumor spread was significantly more extended in group with NRS≥3 than among patients with NRS<3 (p < 0.05). In malnourished patients complete resection rate was significantly decreased (31% vs. 69%, p < 0.001) and they required more often a colo- or ileostoma (17% vs. 6%, p = 0.041). Malnourished patients suffered more often from post-operative complications (62% vs. 37%, p < 0.05), especially infectious like pneumonia or sepsis. All postoperative mortality events (3 cases) occurred in the malnourished group. Conclusions: Malnourished ovarian cancer patients have significantly more often post-operative complications. They suffer from more extended tumor spread and were less frequently postoperatively tumor-free. Based on our results further prospective trials of preoperative nutritional therapy to improve surgical outcome are warranted.

No significant financial relationships to disclose.

Association of the LHON 13,708 and 15,257 mitochondrial DNA mutations with neurodegenerative diseases distinct from LHON

300 patients suffering from neurodegenerative diseases distinct from Leber hereditary optic neuropathy (LHON) were screened for the presence of mitochondrial DNA mutations. We report on nine patients, eight female and one male, who all harboured mutations at positions 13,708 and 15,257 of the mitochondrial DNA. Both mutations have previously been claimed to be associated with LHON. Based on our results, these mutations occur in a number of different neurodegenerative diseases and therefore cannot be regarded as "LHON" mutations.

IMBAS-MS Discovers Organ-Specific HLA Peptide Patterns in Plasma

Distinction of non-self from self is the major task of the immune system. Immunopeptidomics studies the peptide repertoire presented by the human leukocyte antigen (HLA) protein, usually on tissues. However, HLA peptides are also bound to plasma soluble HLA (sHLA), but little is known about their origin and potential for biomarker discovery in this readily available biofluid. Currently, immunopeptidomics is hampered by complex workflows and limited sensitivity, typically requiring several mL of plasma. Here, we take advantage of recent improvements in the throughput and sensitivity of mass spectrometry (MS)-based proteomics to develop a highly sensitive, automated, and economical workflow for HLA peptide analysis, termed Immunopeptidomics by Biotinylated Antibodies and Streptavidin (IMBAS). IMBAS-MS quantifies more than 5000 HLA class I peptides from only 200 μl of plasma, in just 30 min. Our technology revealed that the plasma immunopeptidome of healthy donors is remarkably stable throughout the year and strongly correlated between individuals with overlapping HLA types. Immunopeptides originating from diverse tissues, including the brain, are proportionately represented. We conclude that sHLAs are a promising avenue for immunology and potentially for precision oncology.

An accessible workflow for high-sensitivity proteomics using parallel accumulation-serial fragmentation (PASEF)

Deep and accurate proteome analysis is crucial for understanding cellular processes and disease mechanisms; however, it is challenging to implement in routine settings. In this protocol, we combine a robust chromatographic platform with a high-performance mass spectrometric setup to enable routine yet in-depth proteome coverage for a broad community. This entails tip-based sample preparation and pre-formed gradients (Evosep One) combined with a trapped ion mobility time-of-flight mass spectrometer (timsTOF, Bruker). The timsTOF enables parallel accumulation-serial fragmentation (PASEF), in which ions are accumulated and separated by their ion mobility, maximizing ion usage and simplifying spectra. Combined with data-independent acquisition (DIA), it offers high peak sampling rates and near-complete ion coverage. Here, we explain how to balance quantitative accuracy, specificity, proteome coverage and sensitivity by choosing the best PASEF and DIA method parameters. The protocol describes how to set up the liquid chromatography-mass spectrometry system and enables PASEF method generation and evaluation for varied samples by using the py_diAID tool to optimally position isolation windows in the mass-to-charge and ion mobility space. Biological projects (e.g., triplicate proteome analysis in two conditions) can be performed in 3 d with ~3 h of hands-on time and minimal marginal cost. This results in reproducible quantification of 7,000 proteins in a human cancer cell line in quadruplicate 21-min injections and 29,000 phosphosites for phospho-enriched quadruplicates. Synchro-PASEF, a highly efficient, specific and novel scan mode, can be analyzed by Spectronaut or AlphaDIA, resulting in superior quantitative reproducibility because of its high sampling efficiency.