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ProteomicsMassSpecPreppy - an end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics applications
In proteomics, fast, efficient and highly reproducible sample preparation are of utmost importance, particularly in view of fast scanning mass spectrometers enabling analyses of large sample series. To address this need, we have developed the web application MassSpecPreppy that operates on the open ...
ORGANISM(S): Saccharomyces Cerevisiae Strain C13-aby.s86 Escherichia Coli K-12 (ncbitaxon:83333) Homo Sapiens (ncbitaxon:9606) 
2023-07-20 | MSV000092489 | MassIVE
ProteomicsIn-Depth Comparison of Reagent-Based Digestion Methods and Two Commercially Available Kits for Bottom-Up Proteomics
We assessed two physical disruption methods to homogenize cells —sonication and BeatBox—alongside four digestion protocols. Two of them are lab-reagent strategies: urea-based, and SDC (Sodium deoxycholate)-based in-solution digestion, and two are commercially available kits: the EasyPep kit from The...
ORGANISM(S): Homo sapiens (Human) 
2026-01-07 | PXD056409 | Pride
In-solution digestion Lc-ms Proteomics Proteolysis Bottom-up proteomics 
ProteomicsInfluence of digestion protocol in Protein Quantitation
Quantitative determination of absolute and relative protein amounts is an essential requirement for most current bottom-up proteomics applications, but protein quantitation estimates are affected by several sources of variability such as sample preparation, mass spectrometric acquisition, and data a...
ORGANISM(S): Escherichia coli 
2014-07-30 | PXD001187 | Pride
Protein quantitation Digestion protocols Fasp 
ProteomicsMS analysis of SARS-CoV2 proteins from patient samples
We developed a simple, MS-based method to specifically detect SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients. Our protocol consists of an acetone precipitation and tryptic digestion of proteins contained within the gargle solution, followed by a targeted MS analysis. Our metho...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-07-16 | MSV000085761 | MassIVE
ProteomicsComparison of in-solution and SP3 sample processing workflows on HeLa cell samples
Comparison of in-solution and single-pot, solid-phase-enchanced sample preparation (SP3) sample processing workflows on HeLa cell samples, using different lysis buffers based on SDS and guanidine hydrochloride, for optimal analysis by liquid chromatography mass spectrometry (LC-MS)
ORGANISM(S): Homo sapiens (Human) 
2022-08-12 | PXD031918 | Pride
Proteomics Lc-ms Hela Sp3 In-solution digestion 
ProteomicsSerial In-solution digestion protocol for mass spectrometry-based glycomics and proteomics analysis
Advancement in mass spectrometry has revolutionised the field of proteomics. However, there remains a gap in the analysis of protein post-translational modifications (PTMs), particularly for glycosylation. Glycosylation, the most common form of PTM, is involved in most biological processes; thus, an...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Mus musculus (Mouse) 
2020-04-30 | PXD017513 | Pride
Glycosaminoglycans Proteomics Mass spectrometry Glycomics Proteoglycans Fasp Extracellular matrix. 
ProteomicsUpdated in-gel digestion for protein analysis by mass spectrometry
The in-gel digestion of proteins for analysis by liquid chromatograph mass spectrometry has been used since the early 1990s. Although several improvements have contributed to increasing the quality of the data obtained, many recent publications still use sub-optimal approaches. We present an updated...
ORGANISM(S): Homo sapiens (Human) 
2018-10-02 | PXD009600 | Pride
Proteomics Mass spectrometry In-gel digestion Trypsin 
ProteomicsComparison of SPEED, S-Trap, and In-Solution based sample preparation methods for tandem mass spectrometry
Bottom-up proteomic analyses rely on efficient protein extraction from tissue and proteolysis into peptides for mass spectrometry. Commonly used detergent-based strategies aid cell lysis and protein solubilization but are poorly compatible with downstream protein digestion and liquid chromatography-...
ORGANISM(S): Ovis aries 
2023-03-30 | PXD030796 | Pride
Speed Plasma Kidney Sheep Swath-ms Tripletof S-trap 
ProteomicsComparison of SPEED, S-Trap, and In-Solution based sample preparation methods for tandem mass spectrometry
Bottom-up proteomic analyses rely on efficient protein extraction from tissue and proteolysis into peptides for mass spectrometry. Commonly used detergent-based strategies aid cell lysis and protein solubilization but are poorly compatible with downstream protein digestion and liquid chromatography-...
ORGANISM(S): Ovis aries 
2023-03-30 | PXD030797 | Pride
Speed Plasma Kidney Sheep Tripletof S-trap Dda 
OtherInfluence of the Digestion Technique, Protease, and Missed Cleavage Peptides in Protein Quantitation.
Data from ProteomeXchange, PXD ID: PXD001187. Enzyme: LysC_Trypsin, file: 121219_S_CCES_01_03_LysC_Try_1to10_Mixt_1_3.mzXML. Published as part of J Proteome Res. 2014 Jul 28 . From the Abstract: {{i}} Here we evaluated both in-solution and filter-aided digestion protocols and assessed their influen...
ORGANISM(S): Enterobacteria_phage_13a_uid30603,enterobacteria_phage_933w_uid14043,enterobacteria_phage_alpha3_uid14570,enterobacteria_phage_ba14_uid30599,enterobacteria_phage_bp_4795_uid14287,enterobacteria_phage_bz13_uid14635,enterobacteria_phage_cdti_uid19737,enterobacteria_phage_ecods1_uid30601,enterobacteria_phage_eps7_uid29287,enterobacteria_phage_epsilon15_uid14285,enterobacteria_phage_es18_uid15174,enterobacteria_phage_felix_01_uid14323,enterobacteria_phage_fels_2_uid32273,enterobacteria_phage_fi_sensu_lato_uid15459,enterobacteria_phage_g4_sensu_lato_uid14318,enterobacteria_phage_hk022_uid14048,enterobacteria_phage_hk620_uid14115,enterobacteria_phage_hk97_uid14592,enterobacteria_phage_i2_2_uid14572,enterobacteria_phage_id18_sensu_lato_uid16628,enterobacteria_phage_id2_moscow_id_2001_uid16591,enterobacteria_phage_if1_uid14039,enterobacteria_phage_ike_uid14627,enterobacteria_phage_ime08_uid50177,enterobacteria_phage_jk06_uid15569,enterobacteria_phage_js10_uid38265,enterobacteria_phage_js98_uid27983,enterobacteria_phage_jse_uid38263,enterobacteria_phage_k1e_uid16228,enterobacteria_phage_k1f_uid15880,enterobacteria_phage_k1_5_uid17059,enterobacteria_phage_lambda_uid14204,enterobacteria_phage_m13_uid14549,enterobacteria_phage_min27_uid29143,enterobacteria_phage_ms2_uid14659,enterobacteria_phage_mu_uid14105,enterobacteria_phage_n15_uid14086,enterobacteria_phage_n4_uid18511,enterobacteria_phage_p1_uid14493,enterobacteria_phage_p22_uid14478,enterobacteria_phage_p2_uid14035,enterobacteria_phage_p4_uid14414,enterobacteria_phage_phi1_uid20789,enterobacteria_phage_phieco32_uid28729,enterobacteria_phage_phiecom_gj1_uid27979,enterobacteria_phage_phip27_uid14599,enterobacteria_phage_phiv10_uid16381,enterobacteria_phage_phix174_sensu_lato_uid14015,enterobacteria_phage_prd1_uid14062,enterobacteria_phage_psp3_uid14345,enterobacteria_phage_rb14_uid37825,enterobacteria_phage_rb16_uid51699,enterobacteria_phage_rb32_uid17997,enterobacteria_phage_rb43_uid15417,enterobacteria_phage_rb49_uid14301,enterobacteria_phage_rb51_uid37819,enterobacteria_phage_rb69_uid15141,enterobacteria_phage_rtp_uid16178,enterobacteria_phage_sf6_uid14498,enterobacteria_phage_sfv_uid14162,enterobacteria_phage_sp6_uid14291,enterobacteria_phage_ssl_2009a_uid34919,enterobacteria_phage_st104_uid14499,enterobacteria_phage_st64t_uid14230,enterobacteria_phage_st_1_uid38669,enterobacteria_phage_t1_uid14496,enterobacteria_phage_t3_uid14336,enterobacteria_phage_t4_uid14044,enterobacteria_phage_t5_uid15143,enterobacteria_phage_t7_uid14460,enterobacteria_phage_tls_uid19775,enterobacteria_phage_vt2_sakai_uid14480,enterobacteria_phage_wa13_sensu_lato_uid16595,enterobacteria_phage_wv8_uid38281,enterobacteria_phage_yyz_2008_uid32231,enterobacteriophage_qbeta_uid15479, Pxd001187, Escherichia_coli_k_12_substr__mg1655 
GPM32310002602 | GPMDB
Resource Reanalysis 
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