Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD008408/BTIS-BTUM.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD008408/2017-08-29-BTIS_BTUM_Pool_MARS-RF_SwissProt_human_noAAsubst_library__FDR.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD008408/2017-08-29-BTIS_Pools_MARS-RF_SwissProt_human_noAAsubst_library__FDR.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD008408/2017-08-29-BTUM_Pools_MARS-RF__SwissProt_human_noAAsubst_library__FDR.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD008408/2017-08-29-BTIS_Pools_MARS-RF_SwissProt_human_noAAsubst_library_MGFPeaklist.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD008408/2017-08-29-BTUM_Pools_MARS-RF__SwissProt_human_noAAsubst_library_MGFPeaklist.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD008408/2017-08-29-BTIS_BTUM_Pool_MARS-RF_SwissProt_human_noAAsubst_library_MGFPeaklist.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD008408/SWATH-clinical.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD008408/2017-08-29-BTIS_BTUM_Pool_MARS-RF_SwissProt_human_noAAsubst_library.groupftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD008408/LIBRARY-BTUM.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD008408/2017-08-29-BTUM_Pools_MARS-RF__SwissProt_human_noAAsubst_library.groupftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD008408/LIBRARY-BTIS.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD008408/2017-08-29-BTIS_Pools_MARS-RF_SwissProt_human_noAAsubst_library.groupprimaryOK200katarzyna.macur@biotech.ug.edu.plAleksandra BoguckaMass SpectrometryShotgun proteomicsSWATH MSBreast CancerNot availableQuantitative proteomicsBreast tumorBreast tissueSwath-msMicrolcFresh frozenhttps://www.ebi.ac.uk/pride/archive/projects/PXD008408Mammary Gland Tumor CellMammary GlandFresh-frozen human normal breast tissue (BTIS) and breast tumor (BTUM) samples from 8 patients undergoing breast cancer surgery were acquired from Central Biobank of Tissue and Genetic Material of the Medical University of Gdansk/Poland and stored at -70°C until the analysis. The tissue and tumor samples were cut and manually grinded in extraction vessel using pistel. Proteins were extracted using buffer that contained: 1% Triton X-100, 2 M thiourea, 5 M urea, 50 mM Tris-HCl pH 7.5, 150 mM NaCl, 2% CHAPS, 0.2% Ampholyte 3-10, 1.5% SB3-10, 1 mM EDTA and 1 mM dithiotreitol (DTT), with sonication. Pool extracts from all investigated BTIS and BTUM samples were also prepared by mixing 20μL aliquots of all invastigated BTIS or BTUM samples, respectively. The extracts were diluted 1:50 with 50mM NH4HCO3 for direct enzymatic digestion. In part of the pool BTIS and BTUM extracts the buffer was exchanged to Multiple Affinity Removal Spin Cartridge Human 14-compatible (MARS-14, Agilent Technologies) buffer by ultrafiltration on 3 kDa Amicon (Merck) filter and by passing through 0.22 µm cellulose acetate membrane (Agilent Technologies). MARS immunodepletion of 14 most abundant proteins in human serum (HAP) in those pool samples was performed according to manufacturer's protocol and the buffer was exchanged with 3 kDa Amicon to the trypsin digestion-compatible one. There were two groups of samples: (1) pool BTIS and BTUM samples used for IDA microLC-MS/MS measurements necessary for spectral library creation, consisting of (a) MARS-14-enriched with low abundant proteins fraction, (b) MARS-14-retained 14 HAP (with other bound to HAPs) proteins fraction, (c) pool undepleted BTIS and BTUM samples, and, (2) separate BTIS and BTUM samples from individual patients for which data-independent acquisition microLC-MS/MS SWATH quantitative measurements were performed. All the samples were reduced with 10 mM DTT in 56°C for 30 min. After cooling down, they were incubated with 20 mM iodoacetamide in darkness at room temperature for 30min. Trypsin digestion (1:50 enzyme to substrate ratio) was carried out in 37°C for 19h and then stopped by lowering the pH to 3 with the use of 5% formic acid (FA)/acetonitrile (ACN). Samples were evaporated (SpeedVac), reconstituted in 50µl of 0.5% trifluoroacetic acid in water for Pierce C18 SpinTips (Thermo Scientific) desalting prior to MS analysis. The triplicate elutions of the desalted samples were carried out to 30, 50 and 80% ACN/0.1%FA in water. Resulting eluates from the same samples were collected to the same tubes, evaporated to dryness (SpeedVac), reconstituted in 30 µl of 50% ACN/0.1% FA in water and subjected to microLC-MS/MS measurements. The 5µl of each sample was injected onto the column using the CTC Pal Autosampler. The samples were separated on the ChromXP C18CL microLC columns (150 x 0.3 mm, 3 µm, 120 Å, Eksigent) with the Ekspert microLC 200 System (Eksigent) using a gradient elution from 10 to 90% mobile phase B (mobile phases: A: 0.1% FA in water, B: 0,1% FA in ACN) in 30 min, at a flow rate of 10 µL/min. Eluate from the column was analyzed in a positive ion mode on a TripleTOF® 5600+ system with DuoSpray Ion Source (SCIEX). The system was controlled by the Analyst TF 1.7.1 software (SCIEX). The samples for spectral library creation were subjected to shotgun MS experiment using the following IDA parameters: TOF MS survey scan in the m/z range of 100-2,000 for 50 ms with the top 10 precursor ions (+2 to +5) selected for collision-induced dissociation (CID) fragmentation. Each experiment was conducted with rolling collision energy and the precursor ions were excluded from reselection for 5 s after two occurrences. Product ion spectra were collected in the m/z range of 100-2,000 for 40 ms, resulting in a duty cycle of 1.11s. Then, the separate patients’ samples were analyzed using the data-independent SWATH-MS mode. The analyses were executed in a looped product ion mode with the following instrument settings: 25 overlapping transmission windows (25 Da wide) covering the precursor m/z of 400-1,000; SWATH product ion scans acquired in the m/z of 100-2,000. The collision energy for each window was calculated for a +2 to +5 ions centered upon the window with a spread of 2. The SWATH-MS1 survey scans were acquired in high sensitivity mode in the m/z range of 100-2,000 for 50 ms and followed by 40 ms high sensitivity product ion scans, which resulted in the total cycle time of 1.11s.PrideProtein database searches were conducted in Protein Pilot 4.5 Software (SCIEX) with the Paragon algorithm against the SwissProt Homo sapiens database (ver. 31.07.2017, 20 214 entries) with automated false discovery rate using the following parameters: instrument TripleTOF 5600, trypsin digestion, iodoacetamide alkylation, ID focus on biological modifications, “thorough ID” search effort, and detected protein threshold [Conf] > 10%. Three searches were performed: (1) control breast tissue pools’ samples (unfractionated and fractionated by MARS-14 kit), (2) breast tumor pools’ samples (unfractionated and fractionted by MARS-14 kit), and (3) a comprehensive search of all mentioned samples, which constituted spectral library for further quantitative studies. A resulting .group file was loaded into MS/MS All with SWATH Acquisition MicroApp 2.01 in PeakView 2.2 (SCIEX) to automatically create a spectral library with following parameters: modified peptides allowed, and shared peptides excluded. 144 files of SWATH-MS measurements of individual clinical samples were subsequently loaded into the software to be analyzed with the created spectral library. Primary settings for data processing were: maximum 6 transitions per peptide, 95% peptide confidence, peptide FDR < 1%, extraction window of 10 minutes and XIC width of 75 ppm. All valid peptides were processed by the software automatically, and minimum of 2 and maximum of 6 peptides (with unique sequence) with best scores resulting from automatic evaluation were chosen for each protein to export data.ProteomicsKatarzyna MacurLaboratory of Mass Spectrometry, Core Facility Laboratories, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of GdanskPARTIALHomo Sapiens (human)aleksandra.lewandowska@biotech.ug.edu.pl41797989 Macur K, Bogucka AE, Fel-Tukalska A, Skokowski J, Ołdziej S, Czaplewska P. A label-free microLC-SWATH-MS methodology with immunoaffinity depletion of highly abundant serum proteins for quantitative proteomic comparison of fresh-frozen human normal breast tissue and tumor clinical specimens. Front Mol Biosci. 2026 13:1739472 10.3389/fmolb.2026.1739472BiomedicalJustus Liebig University GiessenGermanyfalseQuantitative proteomic analysis of fresh-frozen human breast tissue and tumor samples using microLC-SWATH-MSFuture improvements in the field of breast cancer prevention, diagnosis and treatment require deeper knowledge and better understanding of the molecular processes and signaling pathways that lead to the transformation of normal cells to cancer ones and the disease progression. Quantitative proteome profiling of fresh frozen breast tissue and tumor samples may accelerate and facilitate this process. Liquid chromatography (LC) hyphenated to tandem mass spectrometry (MS/MS) technique in data-independent SWATH acquisition mode is a powerful tool for such profiling, because all the precursor ions are fragmented there, which enables label-free identification and quantification of theoretically all proteins in the sample. In this study we performed microLC separation before SWATH-MS analysis. The spectral library, which is necessary for SWATH quantification of the investigated samples, consisted of proteins identified by protein database search of the MS/MS spectra obtained by the information-dependent acquisition (IDA) screening of both normal human breast tissue and breast tumor samples, which were additionally enriched in low abundant proteins by immunoaffinity depletion from 14 high abundant serum proteins. Using the described methodology we detected 547 proteins in all qualitative experiments, which served then as a spectral library for further label-free SWATH quantification of separate breast tumor and corresponding normal breast tissue samples of 8 patients. Among them, 299 proteins were successfully quantified. Levels of 188 of them varied significantly (p<0.05) between normal breast tissue and breast tumor samples. 31proteins were up-regulated and 14 were down-regulated at least two fold in breast tumors comparing to normal breast 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